FASTQ Sequence and Sequence Quality Format
FASTQ is a text-based file format for sharing sequencing data combining both the sequence and an associated per base quality score.
Description
More detailed information about this field from each metasource.
FASTQ is a text-based file format for sharing sequencing data combining both the sequence and an associated per base quality score.
metasource: Fairsharing.orgversion: FAIRsharing.org: FASTQ Sequence and Sequence Quality Format; FASTQ Sequence and Sequence Quality Format; DOI: https://doi.org/10.25504/FAIRsharing.r2ts5t; Last edited: April 27, 2021, 8:02 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
Webpage:
http://news.open-bio.org/news/2009/12/nar-fastq-format/Webpage
More detailed information about this field from each metasource.
http://news.open-bio.org/news/2009/12/nar-fastq-format/
metasource: Fairsharing.orgversion: FAIRsharing.org: FASTQ Sequence and Sequence Quality Format; FASTQ Sequence and Sequence Quality Format; DOI: https://doi.org/10.25504/FAIRsharing.r2ts5t; Last edited: April 27, 2021, 8:02 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
PMID: 20015970
metasource: Fairsharing.org
version: FAIRsharing.org: FASTQ Sequence and Sequence Quality Format; FASTQ Sequence and Sequence Quality Format; DOI: https://doi.org/10.25504/FAIRsharing.r2ts5t; Last edited: April 27, 2021, 8:02 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
Publications
More detailed information about this field from each metasource.
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
PMID: 20015970
metasource: Fairsharing.org
version: FAIRsharing.org: FASTQ Sequence and Sequence Quality Format; FASTQ Sequence and Sequence Quality Format; DOI: https://doi.org/10.25504/FAIRsharing.r2ts5t; Last edited: April 27, 2021, 8:02 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
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The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
PubMed citations: 454.
454 articles citing: The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
The complete chloroplast genome sequences of Aster souliei Franch and Aster tongolensis Franch (Asteraceae). PMID:35342796
A comparison of transcriptome analysis methods with reference genome. PMID:35337265
Mitochondrial genome of Bulinus truncatus (Gastropoda: Lymnaeoidea): Implications for snail systematics and schistosome epidemiology. PMID:35284876
Modifying Anthocyanins Biosynthesis in Tomato Hairy Roots: A Test Bed for Plant Resistance to Ionizing Radiation and Antioxidant Properties in Space. PMID:35283922
Green walnut husk extracts Proliferation and Migration in Gastric Cancer. PMID:35281866
Identification of sleep fragmentation-induced gut microbiota alteration and prediction of functional impact in Sprague Dawley rats harboring microbiome derived from multiple human donors. PMID:35273743
Chromosome-scale Echinococcus granulosus (genotype G1) genome reveals the Eg95 gene family and conservation of the EG95-vaccine molecule. PMID:35241789
Genome-wide transcriptome analysis of porcine epidemic diarrhea virus virulent or avirulent strain-infected porcine small intestinal epithelial cells. PMID:35234615
FXR1 can bind with the CFIm25/CFIm68 complex and promote the progression of urothelial carcinoma of the bladder by stabilizing TRAF1 mRNA. PMID:35194031
The induction of peripheral trained immunity in the pancreas incites anti-tumor activity to control pancreatic cancer progression. PMID:35140221
Characterization of the microRNA Expression Profiles in the Goat Kid Liver. PMID:35082837
Comparative analysis of protein-protein interaction networks in metastatic breast cancer. PMID:35045088
De novo transcriptome sequencing of the northern fowl mite, Ornithonyssus sylviarum, shed light on parasitiform poultry mites evolution and its chemoreceptor repertoires. PMID:35032220
De Novo Transcriptome Analysis of the Venom of Latrodectus geometricus with the Discovery of an Insect-Selective Na Channel Modulator. PMID:35011282
Ploidy level enhances the photosynthetic capacity of a tetraploid variety of Acer buergerianum Miq. PMID:35003928
Distinguishing Relapse From Reinfection With Whole-Genome Sequencing in Recurrent Pulmonary Tuberculosis: A Retrospective Cohort Study in Beijing, China. PMID:34956119
Combined Transcriptome and Metabolome Analysis of Alfalfa Response to Thrips Infection. PMID:34946916
Antagonistic Effects of Enrofloxacin on Carbendazim-Induced Developmental Toxicity in Zebrafish Embryos. PMID:34941783
Intellectual disability genomics: current state, pitfalls and future challenges. PMID:34930158
Complete Chloroplast Genome Sequence of Erigeron breviscapus and Characterization of Chloroplast Regulatory Elements. PMID:34899783
Complete chloroplast genome sequence and phylogenetic analysis of Ilex pernyi Franch. PMID:34869882
A two-adjuvant multiantigen candidate vaccine induces superior protective immune responses against SARS-CoV-2 challenge. PMID:34863353
Identification of the Important Genes of Bradyrhizobium diazoefficiens 113-2 Involved in Soybean Nodule Development and Senescence. PMID:34858367
Mixed Transcriptome Analysis Revealed the Possible Interaction Mechanisms between Zizania latifolia and Ustilago esculenta Inducing Jiaobai Stem-Gall Formation. PMID:34830140
Invasive atypical non-typhoidal Salmonella serovars in The Gambia. PMID:34812716
Analyzing differentially expressed genes and pathways of Bex2-deficient mouse lung via RNA-Seq. PMID:34803456
Endothelial eNAMPT drives EndMT and preclinical PH: rescue by an eNAMPT-neutralizing mAb. PMID:34790349
Transcriptome Profiling of Duodenum Reveals the Importance of Boron Supplementation in Modulating Immune Activities in Rats. PMID:34773147
Functional genomics data: privacy risk assessment and technological mitigation. PMID:34759381
Emerging and Established Trends to Support Secure Health Information Exchange. PMID:34713107
Genome-wide analyses of light-regulated genes in Aspergillus nidulans reveal a complex interplay between different photoreceptors and novel photoreceptor functions. PMID:34679095
Comparative transcriptome provides insights into the selection adaptation between wild and farmed foxes. PMID:34646484
Mechanism of the Passage of Angiostrongylus cantonensis across the Final Host Blood-Brain Barrier Using the Next-Generation Sequencing. PMID:34630591
Genome-Wide Transcriptional Changes of Rhodosporidium kratochvilovae at Low Temperature. PMID:34603256
Differences in Acid Stress Response of Lacticaseibacillus paracasei Zhang Cultured from Solid-State Fermentation and Liquid-State Fermentation. PMID:34576848
RNA-Seq-Based Profiling of pl Mutant Reveals Transcriptional Regulation of Anthocyanin Biosynthesis in Rice (Oryza sativa L.). PMID:34575968
Circulating microRNAs in Early Breast Cancer Patients and Its Association With Lymph Node Metastases. PMID:34513655
Challenges for the standardized reporting of NGS HLA genotyping: Surveying gaps between clinical and research laboratories. PMID:34479742
Development of a defined medium for Corynebacterium glutamicum using urea as nitrogen source. PMID:34471588
Statistical guidelines for quality control of next-generation sequencing techniques. PMID:34462322
RNA Sequencing Analyses for Deciphering Potato Molecular Responses. PMID:34448155
Transcriptional Profiling and Functional Analysis of N1/N2 Neutrophils Reveal an Immunomodulatory Effect of S100A9-Blockade on the Pro-Inflammatory N1 Subpopulation. PMID:34447377
Identification of Novel lncRNA and Differentially Expressed Genes (DEGs) of Testicular Tissues among Cattle, Yak, and Cattle-Yak Associated with Male Infertility. PMID:34438876
Computational resources to define alleles and altered regulatory motifs at genomically edited candidate response elements. PMID:34417596
Transcriptome Analysis of Flower Development and Mining of Genes Related to Flowering Time in Tomato (Solanum lycopersicum). PMID:34360893
Bottleneck size and selection level reproducibly impact evolution of antibiotic resistance. PMID:34312522
Empirical evaluation of methods for de novo genome assembly. PMID:34307867
Transcriptome Characterization and Identification of Molecular Markers (SNP, SSR, and Indels) in the Medicinal Plant Sarcandra glabra spp. PMID:34307686
Mesenchymal stem cell-derived exosomes protect trabecular meshwork from oxidative stress. PMID:34290351
Cotinine Hydroxylase CotA Initiates Biodegradation of Wastewater Micropollutant Cotinine in Nocardioides sp. Strain JQ2195. PMID:34232707
Impairment of neuronal mitochondrial function by L-DOPA in the absence of oxygen-dependent auto-oxidation and oxidative cell damage. PMID:34226525
Differentially Expressed MiRNAs of Goat Submandibular Glands Among Three Developmental Stages Are Involved in Immune Functions. PMID:34211501
Candidate l-methionine target piRNA regulatory networks analysis response to cocaine-conditioned place preference in mice. PMID:34196487
Implications of Climate Change: How Does Increased Water Temperature Influence Biofilm and Water Quality of Chlorinated Drinking Water Distribution Systems? PMID:34168627
Chromosome-Scale Genome Assembly of the Resurrection Plant Acanthochlamys bracteata (Velloziaceae). PMID:34165527
Circulating miR-19a-3p and miR-19b-3p characterize the human aging process and their isomiRs associate with healthy status at extreme ages. PMID:34160893
The complete chloroplast genome of Cymbidium dayanum (Orchidaceae). PMID:34151012
Involvement of eNAMPT/TLR4 signaling in murine radiation pneumonitis: protection by eNAMPT neutralization. PMID:34139379
Canonical NF-κB signaling maintains corneal epithelial integrity and prevents corneal aging via retinoic acid. PMID:34085926
MPRAdecoder: Processing of the Raw MPRA Data With a priori Unknown Sequences of the Region of Interest and Associated Barcodes. PMID:34046055
Chromosomal characteristics of salt stress heritable gene expression in the rice genome. PMID:34044788
Genome Recovery, Functional Profiling, and Taxonomic Classification from Metagenomes. PMID:33961223
Complement C3a activates osteoclasts by regulating the PI3K/PDK1/SGK3 pathway in patients with multiple myeloma. PMID:33960177
SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses. PMID:33932985
A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses. PMID:33920047
Transcriptional Landscape of Vero E6 Cells during Early Swine Acute Diarrhea Syndrome Coronavirus Infection. PMID:33919952
Next-Generation Sequencing Reveals That Oxidative Phosphorylation Might Be a Key Pathway Differently Expressed in the Third and Fourth Stages Larvae of Angiostrongylus cantonensis. PMID:33884016
Complete Genome Sequence of Campylobacter coli Bacteriophage CAM-P21. PMID:33858930
fqfa: A pure Python package for genomic sequence files. PMID:33855258
Single-Cell RNA Sequencing Analysis: A Step-by-Step Overview. PMID:33835452
Comparative Transcriptome and Expression Profiling of Resistant and Susceptible Banana Cultivars during Infection by Fusarium oxysporum. PMID:33809411
Resequencing of Microbial Isolates: A Lab Module to Introduce Novices to Command-Line Bioinformatics. PMID:33796082
Transcriptome analysis of the impact of exogenous methyl jasmonate on the opening of sorghum florets. PMID:33788892
Activation of Toll-Like Receptor 7 Signaling Pathway in Primary Sjögren's Syndrome-Associated Thrombocytopenia. PMID:33767707
Genome-resolved metagenomics using environmental and clinical samples. PMID:33758906
Named Data Networking for Genomics Data Management and Integrated Workflows. PMID:33748749
Horizontal Gene Transfer and Gene Duplication of β-Fructofuranosidase Confer Lepidopteran Insects Metabolic Benefits. PMID:33739418
Methylation of rRNA as a host defense against rampant group II intron retrotransposition. PMID:33678171
Nanopore Sequencing Resolves Elusive Long Tandem-Repeat Regions in Mitochondrial Genomes. PMID:33670420
Processing and Analysis of RNA-seq Data from Public Resources. PMID:33606253
Comparative Transcriptome Analysis of Streptomyces nodosus Mutant With a High-Yield Amphotericin B. PMID:33598451
Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types. PMID:33408878
HAPHPIPE: Haplotype Reconstruction and Phylodynamics for Deep Sequencing of Intrahost Viral Populations. PMID:33367849
Phase 1 study of belinostat (PXD-101) and bortezomib (Velcade, PS-341) in patients with relapsed or refractory acute leukemia and myelodysplastic syndrome. PMID:33356689
MicroRNA-1291 Is Associated With Locoregional Metastases in Patients With Early-Stage Breast Cancer. PMID:33343622
Phylogenetic Analysis of Mitogenomic Data Sets Resolves the Relationship of Seven Macropostrongyloides Species from Australian Macropodid and Vombatid Marsupials. PMID:33322694
Integrated Physiological and Transcriptomic Analyses Reveal a Regulatory Network of Anthocyanin Metabolism Contributing to the Ornamental Value in a Novel Hybrid Cultivar of Camellia Japonica. PMID:33297392
Long non-coding RNA expression profiles in peripheral blood mononuclear cells of patients with coronary artery disease. PMID:33282383
RNA sequencing: new technologies and applications in cancer research. PMID:33276803
Transcriptional Remodeling Patterns in Murine Dendritic Cells Infected with Paracoccidioides brasiliensis: More Is Not Necessarily Better. PMID:33255176
Associations Between Maternal Lifetime Stress and Placental Mitochondrial DNA Mutations in an Urban Multiethnic Cohort. PMID:33229036
Transcriptomic dataset of cultivated (Sesamum indicum), wild (S. mulayanum), and interspecific hybrid sesame in response to induced Macrophomina phaseolina infection. PMID:33134450
Polyethylene Glycol-Coated Graphene Oxide Loaded with Erlotinib as an Effective Therapeutic Agent for Treating Nasopharyngeal Cancer Cells. PMID:33116488
Differential Analysis of Stress Tolerance and Transcriptome of Probiotic Lacticaseibacillus casei Zhang Produced from Solid-State (SSF-SW) and Liquid-State (LSF-MRS) Fermentations. PMID:33114487
Comparative morphological and transcriptomic analyses reveal chemosensory genes in the poultry red mite, Dermanyssus gallinae. PMID:33087814
Pharmacological Effects of Novel Peptide Drugs on Allergic Rhinitis at the Small Ribonucleic Acids Level. PMID:33061944
The reuse of public datasets in the life sciences: potential risks and rewards. PMID:33024631
Physiological adaptations to sugar-mimic alkaloids: Insights from Bombyx mori for long-term adaption and short-term response. PMID:33005339
Global transcriptome study of Dip2B-deficient mouse embryonic lung fibroblast reveals its important roles in cell proliferation and development. PMID:33005301
PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores. PMID:32976553
Transcriptome of peanut kernel and shell reveals the mechanism of calcium on peanut pod development. PMID:32973268
Statistical and Bioinformatics Analysis of Data from Bulk and Single-Cell RNA Sequencing Experiments. PMID:32926366
Assessing the Impact of Data Preprocessing on Analyzing Next Generation Sequencing Data. PMID:32850708
Periplaneta americana Extracts Accelerate Liver Regeneration via a Complex Network of Pathways. PMID:32848780
First record of a tandem-repeat region within the mitochondrial genome of Clonorchis sinensis using a long-read sequencing approach. PMID:32845881
Bioenergetic defects in muscle fibers of RYR1 mutant knock-in mice associated with malignant hyperthermia. PMID:32826313
Marked mitochondrial genetic variation in individuals and populations of the carcinogenic liver fluke Clonorchis sinensis. PMID:32813714
Targeted bisulfite sequencing for biomarker discovery. PMID:32755621
Responsible, practical genomic data sharing that accelerates research. PMID:32694666
Identification of BBX proteins as rate-limiting cofactors of HY5. PMID:32661279
Comparative Transcriptome Analysis of Two Contrasting Soybean Varieties in Response to Aluminum Toxicity. PMID:32560405
Pseudouridylation defect due to DKC1 and NOP10 mutations causes nephrotic syndrome with cataracts, hearing impairment, and enterocolitis. PMID:32554502
Caloric restriction attenuates C57BL/6 J mouse lung injury and extra-pulmonary toxicity induced by real ambient particulate matter exposure. PMID:32503629
Transcriptome Analysis of Maternal Gene Transcripts in Unfertilized Eggs of Misgurnus anguillicaudatus and Identification of Immune-Related Maternal Genes. PMID:32485896
CSI NGS Portal: An Online Platform for Automated NGS Data Analysis and Sharing. PMID:32481589
Integrative Analysis of Differential lncRNA/mRNA Expression Profiling in Helicobacter pylori Infection-Associated Gastric Carcinogenesis. PMID:32457731
Transcriptome Analysis Reveals the Flexibility of Cordycepin Network in Cordyceps militaris Activated by L-Alanine Addition. PMID:32390960
MaRe: Processing Big Data with application containers on Apache Spark. PMID:32369166
Dual Recognition of H3K4me3 and DNA by the ISWI Component ARID5 Regulates the Floral Transition in Arabidopsis. PMID:32358072
Phased nucleotide inserts for sequencing low-diversity RNA samples from in vitro selection experiments. PMID:32300045
Comparative Genomics and Transcriptomics Analyses Reveal a Unique Environmental Adaptability of Vibrio fujianensis. PMID:32294952
Effects of High-Dose Ionizing Radiation in Human Gene Expression: A Meta-Analysis. PMID:32178397
Integrated Transcriptomic and Un-Targeted Metabolomics Analysis Reveals Mulberry Fruit (Morus atropurpurea) in Response to Sclerotiniose Pathogen Ciboria shiraiana Infection. PMID:32150966
Microbial community analysis using high-throughput sequencing technology: a beginner's guide for microbiologists. PMID:32108314
Transcriptomic analysis of the testicular fusion in Spodoptera litura. PMID:32075574
Comparative Transcriptomics Reveals Features and Possible Mechanisms of Glucose-Mediated Soil Fungistasis Relief in Arthrobotrys oligospora. PMID:32038576
A Fast and Scalable Workflow for SNPs Detection in Genome Sequences Using Hadoop Map-Reduce. PMID:32033366
Organizing genome engineering for the gigabase scale. PMID:32019919
AMLVaran: a software approach to implement variant analysis of targeted NGS sequencing data in an oncological care setting. PMID:32019565
Integrated mRNA and miRNA transcriptome analysis reveals a regulatory network for tuber expansion in Chinese yam (Dioscorea opposita). PMID:32013881
Comparative transcriptome analysis reveals the response mechanism of Cf-16-mediated resistance to Cladosporium fulvum infection in tomato. PMID:31959099
FQSqueezer: k-mer-based compression of sequencing data. PMID:31953467
Comparative analysis of primary metabolites and transcriptome changes between ungrafted and pumpkin-grafted watermelon during fruit development. PMID:31934503
Temporal and region-specific effects of sleep fragmentation on gut microbiota and intestinal morphology in Sprague Dawley rats. PMID:31924109
Tissue-specific gene expression and protein abundance patterns are associated with fractionation bias in maize. PMID:31900107
Liver Transcriptome Changes of Hyla Rabbit in Response to Chronic Heat Stress. PMID:31847222
Altered microRNA and target gene expression related to Tetralogy of Fallot. PMID:31836860
A comprehensive resource for retrieving, visualizing, and integrating functional genomics data. PMID:31818883
Transcriptomic Analysis of Viable but Non-Culturable Escherichia coli O157:H7 Formation Induced by Low Temperature. PMID:31801285
Host-mediated microbiome engineering (HMME) of drought tolerance in the wheat rhizosphere. PMID:31800619
MS CD49d+CD154+ Lymphocytes Reprogram Oligodendrocytes into Immune Reactive Cells Affecting CNS Regeneration. PMID:31775315
Transcriptome Profiling Unravels a Vital Role of Pectin and Pectinase in Anther Dehiscence in Chrysanthemum. PMID:31766739
LFastqC: A lossless non-reference-based FASTQ compressor. PMID:31725736
Study of the Differentially Expressed Genes in the Pomacea canaliculata Transcriptome after Treatment with Pedunsaponin A. PMID:31698793
A beginner's guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing. PMID:31697321
The Many Faces of Gene Regulation in Cancer: A Computational Oncogenomics Outlook. PMID:31671657
Identification and Expression Analyses of Olfactory Gene Families in the Rice Grasshopper, Oxya chinensis, From Antennal Transcriptomes. PMID:31616318
Identification and characterization of hirudin-HN, a new thrombin inhibitor, from the salivary glands of Hirudo nipponia. PMID:31592161
Weighted Gene Coexpression Network Analysis Identifies Cysteine-Rich Intestinal Protein 1 (CRIP1) as a Prognostic Gene Associated with Relapse in Patients with Acute Myeloid Leukemia. PMID:31577790
High-throughput amplicon sequencing datasets of the metacommunity DNA of the gut microbiota of naturally occurring and laboratory aquaculture green sea urchins Lytechinus variegatus. PMID:31528670
A comprehensive, multidisciplinary, precision medicine approach to discover effective therapy for an undiagnosed, progressive, fibroinflammatory disease. PMID:31520587
Population Dynamics of Salmonella enterica within Beef Cattle Cohorts Followed from Single-Dose Metaphylactic Antibiotic Treatment until Slaughter. PMID:31519659
Identification of heat-tolerance QTLs and high-temperature stress-responsive genes through conventional QTL mapping, QTL-seq and RNA-seq in tomato. PMID:31510927
VAPPER: High-throughput variant antigen profiling in African trypanosomes of livestock. PMID:31494667
Flavonoid Biosynthesis Is Likely More Susceptible to Elevation and Tree Age Than Other Branch Pathways Involved in Phenylpropanoid Biosynthesis in Ginkgo Leaves. PMID:31417595
Comparative Analysis of the Characteristics of Triterpenoid Transcriptome from Different Strains of Wolfiporia cocos. PMID:31362345
A novel pan-cancer biomarker plasma heat shock protein 90alpha and its diagnosis determinants in clinic. PMID:31343810
CCMG practice guideline: laboratory guidelines for next-generation sequencing. PMID:31300550
Morphological, Transcriptomic and Hormonal Characterization of Trimonoecious and Subandroecious Pumpkin (Cucurbita maxima) Suggests Important Roles of Ethylene in Sex Expression. PMID:31261811
De novo transcriptome analysis of Tibetan medicinal plant Dysphania schraderiana. PMID:31259355
Shotgun metagenomic sequencing from Manao-Pee cave, Thailand, reveals insight into the microbial community structure and its metabolic potential. PMID:31248378
Moving Just Enough Deep Sequencing Data to Get the Job Done. PMID:31236009
HumanMycobiomeScan: a new bioinformatics tool for the characterization of the fungal fraction in metagenomic samples. PMID:31202277
Mind the gap: resources required to receive, process and interpret research-returned whole genome data. PMID:31161416
Transcriptome Analysis of Gene Families Involved in Chemosensory Function in Spodoptera littoralis (Lepidoptera: Noctuidae). PMID:31138111
Transcriptional alterations in Caenorhabditis elegans following exposure to an anthelmintic fraction of the plant Picria fel-terrae Lour. PMID:31023350
Transcriptome Dynamics of Double Recessive Mutant, o2o2o16o16, Reveals the Transcriptional Mechanisms in the Increase of Its Lysine and Tryptophan Content in Maize. PMID:31018625
ChimeraMiner: An Improved Chimeric Read Detection Pipeline and Its Application in Single Cell Sequencing. PMID:31010074
Analyzing big datasets of genomic sequences: fast and scalable collection of k-mer statistics. PMID:30999863
GenHap: a novel computational method based on genetic algorithms for haplotype assembly. PMID:30999845
Transcriptome Profiles of Alternaria oxytropis Provides Insights into Swainsonine Biosynthesis. PMID:30988322
Transcriptional Profile Corroborates that bml Mutant Plays likely Role in Premature Leaf Senescence of Rice (Oryza sativa L.). PMID:30959810
Pixel: a content management platform for quantitative omics data. PMID:30944779
Next-generation sequencing of HIV-1 single genome amplicons. PMID:30923677
ChIPulate: A comprehensive ChIP-seq simulation pipeline. PMID:30897079
Comprehensive Analysis of Differentially Expressed mRNA, lncRNA and circRNA and Their ceRNA Networks in the Longissimus Dorsi Muscle of Two Different Pig Breeds. PMID:30836719
De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing. PMID:30816255
Distinct isoforms of Nrf1 diversely regulate different subsets of its cognate target genes. PMID:30814566
Dietary fish oil supplementation alters liver gene expressions to protect against LPS-induced liver injury in weanling piglets. PMID:30782046
SM-RCNV: a statistical method to detect recurrent copy number variations in sequenced samples. PMID:30779024
The Purple Sea Urchin Strongylocentrotus purpuratus Demonstrates a Compartmentalization of Gut Bacterial Microbiota, Predictive Functional Attributes, and Taxonomic Co-Occurrence. PMID:30691133
A Host Factor GPNMB Restricts Porcine Circovirus Type 2 (PCV2) Replication and Interacts With PCV2 ORF5 Protein. PMID:30671053
Isolation of blue-green eggshell pigmentation-related genes from Putian duck through RNA-seq. PMID:30660177
NGmerge: merging paired-end reads via novel empirically-derived models of sequencing errors. PMID:30572828
Characterization of drought stress-responsive root transcriptome of faba bean (Vicia faba L.) using RNA sequencing. PMID:30498675
RNA-Seq transcriptome analysis of breast muscle in Pekin ducks supplemented with the dietary probiotic Clostridium butyricum. PMID:30486769
Toxicity of Melaleuca alternifolia essential oil to the mitochondrion and NAD+/NADH dehydrogenase in Tribolium confusum. PMID:30479882
Identification of Genes that Control Silk Yield by RNA Sequencing Analysis of Silkworm (Bombyx mori) Strains of Variable Silk Yield. PMID:30467288
ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis. PMID:30416717
Detoxification and Immune Transcriptomic Response of the Gill Tissue of Bay Scallop (Argopecten irradians) Following Exposure to the Algicide Palmitoleic Acid. PMID:30404247
Comparative study of gut microbiota in wild and captive Malaysian Mahseer (Tor tambroides). PMID:30353678
Changes in the Fungal Microbiome of Maize During Hermetic Storage in the United States and Kenya. PMID:30333810
Dietary or supplemental fermentable fiber intake reduces the presence of Clostridium XI in mouse intestinal microbiota: The importance of higher fecal bacterial load and density. PMID:30278071
Ethylene-independent promotion of photomorphogenesis in the dark by cytokinin requires COP1 and the CDD complex. PMID:30272197
Data of the first de novo transcriptome assembly of the inflorescence of Curcuma alismatifolia. PMID:30246104
Methylation of High-Risk Human Papillomavirus Genomes Are Associated with Cervical Precancer in HIV-Positive Women. PMID:30237251
Effects of Glyphosate-, Glufosinate- and Flazasulfuron-Based Herbicides on Soil Microorganisms in a Vineyard. PMID:30229276
Comparative RNA-Seq analysis on the regulation of cucumber sex differentiation under different ratios of blue and red light. PMID:30203294
Cellular and molecular characteristics of pollen abortion in chrysanthemum cv. Kingfisher. PMID:30203234
The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information Repositories. PMID:30166985
bioSyntax: syntax highlighting for computational biology. PMID:30134911
Transcriptomic Profiles of Senegalese Sole Infected With Nervous Necrosis Virus Reassortants Presenting Different Degree of Virulence. PMID:30065724
Detoxification- and Immune-Related Transcriptomic Analysis of Gills from Bay Scallops (Argopectenirradians) in Response to Algal Toxin Okadaic Acid. PMID:30060565
Immune-Related Functional Differential Gene Expression in Koi Carp (Cyprinus carpio) after Challenge with Aeromonas sobria. PMID:30036965
Scaling read aligners to hundreds of threads on general-purpose processors. PMID:30020410
The Biological Object Notation (BON): a structured file format for biological data. PMID:29941895
Uncovering global metabolic response to cordycepin production in Cordyceps militaris through transcriptome and genome-scale network-driven analysis. PMID:29915355
Transcriptomic response to GABA-producing Lactobacillus plantarum CGMCC 1.2437T induced by L-MSG. PMID:29894506
Case Report: Identification of an HNF1B p.Arg527Gln mutation in a Maltese patient with atypical early onset diabetes and diabetic nephropathy. PMID:29764441
The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs. PMID:29722807
Diapause in a tropical oil-collecting bee: molecular basis unveiled by RNA-Seq. PMID:29703143
Identification of microRNAs associated with the exogenous spermidine-mediated improvement of high-temperature tolerance in cucumber seedlings (Cucumis sativus L.). PMID:29690862
Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions. PMID:29617724
The Molecular Differentiation of Anatomically Paired Left and Right Mantles of the Pacific Oyster Crassostrea gigas. PMID:29594756
Analyzing Immunoglobulin Repertoires. PMID:29593723
Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations. PMID:29576615
Overcoming erlotinib resistance in EGFR mutation-positive lung adenocarcinomas through repression of phosphoglycerate dehydrogenase. PMID:29556358
OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes. PMID:29463736
Compression of genomic sequencing reads via hash-based reordering: algorithm and analysis. PMID:29444237
Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants. PMID:29438290
Human Papillomavirus DNA Methylation as a Biomarker for Cervical Precancer: Consistency across 12 Genotypes and Potential Impact on Management of HPV-Positive Women. PMID:29420222
SIRT1 regulates Mxd1 during malignant melanoma progression. PMID:29383100
Comparative transcriptome analysis reveals key genes potentially related to soluble sugar and organic acid accumulation in watermelon. PMID:29324867
Deep Illumina sequencing reveals differential expression of long non-coding RNAs in hyperoxia induced bronchopulmonary dysplasia in a rat model. PMID:29312522
Collection and storage of HLA NGS genotyping data for the 17th International HLA and Immunogenetics Workshop. PMID:29247682
Ensemble Modeling Approach Targeting Heterogeneous RNA-Seq data: Application to Melanoma Pseudogenes. PMID:29229974
Whole-exome sequencing for detecting inborn errors of immunity: overview and perspectives. PMID:29225788
CALQ: compression of quality values of aligned sequencing data. PMID:29186284
Transgenerational Effects of Bisphenol A on Gene Expression and DNA Methylation of Imprinted Genes in Brain. PMID:29165653
Mutation accumulation under UV radiation in Escherichia coli. PMID:29109412
The ISB Cancer Genomics Cloud: A Flexible Cloud-Based Platform for Cancer Genomics Research. PMID:29092928
Nasopharyngeal metagenomic deep sequencing data, Lancaster, UK, 2014-2015. PMID:29064471
Xenbase: a genomic, epigenomic and transcriptomic model organism database. PMID:29059324
GeneComp, a new reference-based compressor for SAM files. PMID:29046896
RNA sequencing analysis of activated macrophages treated with the anti-HIV ABX464 in intestinal inflammation. PMID:29039845
Transcriptome and Differential Expression Profiling Analysis of the Mechanism of Ca2+ Regulation in Peanut (Arachis hypogaea) Pod Development. PMID:29033956
Genome-Wide Identification of Transcription Factor-Binding Sites in Quiescent Adult Neural Stem Cells. PMID:29030827
Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. PMID:28985567
Transcriptome Profiling Reveals the Negative Regulation of Multiple Plant Hormone Signaling Pathways Elicited by Overexpression of C-Repeat Binding Factors. PMID:28983312
Transcriptome analysis of mammary epithelial cell gene expression reveals novel roles of the extracellular matrix. PMID:28955800
Gene Regulatory Network for Tapetum Development in Arabidopsis thaliana. PMID:28955355
Genome-wide miRNA response to anacardic acid in breast cancer cells. PMID:28886127
Transcriptomic, biochemical and physio-anatomical investigations shed more light on responses to drought stress in two contrasting sesame genotypes. PMID:28821876
Identification of novel microRNAs in the sheep heart and their regulation in heart failure. PMID:28811555
Transcriptome Analysis of the Sm-Mediated Hypersensitive Response to Stemphylium lycopersici in Tomato. PMID:28769960
Increased sequencing depth does not increase captured diversity of arbuscular mycorrhizal fungi. PMID:28730541
fastQ_brew: module for analysis, preprocessing, and reformatting of FASTQ sequence data. PMID:28701181
Bulked Segregant RNA-seq Reveals Differential Expression and SNPs of Candidate Genes Associated with Waterlogging Tolerance in Maize. PMID:28659961
Transcriptome Analysis of Genes Associated with the Artemisinin Biosynthesis by Jasmonic Acid Treatment under the Light in Artemisia annua. PMID:28642777
A Primer on Infectious Disease Bacterial Genomics. PMID:28590251
Genome annotation for clinical genomic diagnostics: strengths and weaknesses. PMID:28558813
Comparative transcriptome profiling of a thermal resistant vs. sensitive silkworm strain in response to high temperature under stressful humidity condition. PMID:28542312
Genome-wide identification of lncRNAs associated with chlorantraniliprole resistance in diamondback moth Plutella xylostella (L.). PMID:28506253
Enteropathy-associated T cell lymphoma subtypes are characterized by loss of function of SETD2. PMID:28424246
Exploring the Genetic Resistance to Gastrointestinal Nematodes Infection in Goat Using RNA-Sequencing. PMID:28368324
Liver carcinogenesis by FOS-dependent inflammation and cholesterol dysregulation. PMID:28356389
Specific and Novel microRNAs Are Regulated as Response to Fungal Infection in Human Dendritic Cells. PMID:28280489
Integration of EGA secure data access into Galaxy. PMID:28232859
Simulome: a genome sequence and variant simulator. PMID:28186240
Nematophagous fungus Arthrobotrys oligospora mimics olfactory cues of sex and food to lure its nematode prey. PMID:28098555
Genomics pipelines and data integration: challenges and opportunities in the research setting. PMID:28092471
Optimized logic rules reveal interferon-γ-induced modes regulated by histone deacetylases and protein tyrosine phosphatases. PMID:28054346
Transcriptomic analysis reveals the flooding tolerant mechanism in flooding tolerant line and abscisic acid treated soybean. PMID:28012053
A cloud-based workflow to quantify transcript-expression levels in public cancer compendia. PMID:27982081
MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing. PMID:27905885
Sam2bam: High-Performance Framework for NGS Data Preprocessing Tools. PMID:27861637
Lineage-specific roles of the cytoplasmic polyadenylation factor CPEB4 in the regulation of melanoma drivers. PMID:27857118
The PARA-suite: PAR-CLIP specific sequence read simulation and processing. PMID:27812418
VSEARCH: a versatile open source tool for metagenomics. PMID:27781170
From next-generation resequencing reads to a high-quality variant data set. PMID:27759079
SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PMID:27706213
Multi-perspective quality control of Illumina RNA sequencing data analysis. PMID:27687708
Standardization and quality management in next-generation sequencing. PMID:27668169
MetaStorm: A Public Resource for Customizable Metagenomics Annotation. PMID:27632579
SELMAP - SELEX affinity landscape MAPping of transcription factor binding sites using integrated microfluidics. PMID:27628341
Comparison of faecal microbiota in Blastocystis-positive and Blastocystis-negative irritable bowel syndrome patients. PMID:27580855
De Novo Transcriptome Analysis of Differential Functional Gene Expression in Largemouth Bass (Micropterus salmoides) after Challenge with Nocardia seriolae. PMID:27529219
Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). PMID:27442863
PI3K/Akt/mTOR Signaling and Plasma Membrane Proteins Are Implicated in Responsiveness to Adjuvant Dendritic Cell Vaccination for Metastatic Colorectal Cancer. PMID:27435399
The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles. PMID:27368709
Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research. PMID:27297499
Insights into Sexual Precocity of Female Oriental River Prawn Macrobrachium nipponense through Transcriptome Analysis. PMID:27280288
Transcriptome profiles of metamorphosis in the ornamented pygmy frog Microhyla fissipes clarify the functions of thyroid hormone receptors in metamorphosis. PMID:27254593
Generation of mice with longer and better preserved telomeres in the absence of genetic manipulations. PMID:27252083
The A, C, G, and T of Genome Assembly. PMID:27247941
SparkBWA: Speeding Up the Alignment of High-Throughput DNA Sequencing Data. PMID:27182962
Breaking-Cas-interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes. PMID:27166368
fqtools: an efficient software suite for modern FASTQ file manipulation. PMID:27153699
Population Genomic Analysis Reveals Differential Evolutionary Histories and Patterns of Diversity across Subgenomes and Subpopulations of Brassica napus L. PMID:27148342
CARGO: effective format-free compressed storage of genomic information. PMID:27131376
Refined Pichia pastoris reference genome sequence. PMID:27084056
Comparison of transcriptomes of wild-type and isothiazolone-resistant Pseudomonas aeruginosa by using RNA-seq. PMID:27072374
Gut microbiome remodeling induces depressive-like behaviors through a pathway mediated by the host's metabolism. PMID:27067014
Genome-Wide Transcriptional Excavation of Dipsacus asperoides Unmasked both Cryptic Asperosaponin Biosynthetic Genes and SSR Markers. PMID:27066018
Comparison of DNA Quantification Methods for Next Generation Sequencing. PMID:27048884
De Novo Transcriptome Sequencing of Desert Herbaceous Achnatherum splendens (Achnatherum) Seedlings and Identification of Salt Tolerance Genes. PMID:27023614
Quantitative assessment of ribosome drop-off in E. coli. PMID:26935582
Whole-Exome Sequencing Identifies Novel Somatic Mutations in Chinese Breast Cancer Patients. PMID:26870154
Deletion of Na+/H+ exchanger regulatory factor 2 represses colon cancer progress by suppression of Stat3 and CD24. PMID:26867566
PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events. PMID:26758031
Exploring molecular variation in Schistosoma japonicum in China. PMID:26621075
RNA-seq de novo Assembly Reveals Differential Gene Expression in Glossina palpalis gambiensis Infected with Trypanosoma brucei gambiense vs. Non-Infected and Self-Cured Flies. PMID:26617594
Rare Variants in Cardiomyopathy Genes Associated With Stress-Induced Cardiomyopathy. PMID:26606670
Practical guidelines for B-cell receptor repertoire sequencing analysis. PMID:26589402
MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. PMID:26587265
RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes. PMID:26558255
QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles. PMID:26554718
Human genotype-phenotype databases: aims, challenges and opportunities. PMID:26553330
Transcriptomic Analysis of Myocardial Ischemia Using the Blood of Rat. PMID:26540270
NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data. PMID:26460497
Survey of Programs Used to Detect Alternative Splicing Isoforms from Deep Sequencing Data In Silico. PMID:26421304
Minimum information for reporting next generation sequence genotyping (MIRING): Guidelines for reporting HLA and KIR genotyping via next generation sequencing. PMID:26407912
MMBIRFinder: A Tool to Detect Microhomology-Mediated Break-Induced Replication. PMID:26357319
Draft genome of Brugia pahangi: high similarity between B. pahangi and B. malayi. PMID:26350613
NCBI BLAST+ integrated into Galaxy. PMID:26336600
Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud. PMID:26248053
H2O2 production rate in Lactobacillus johnsonii is modulated via the interplay of a heterodimeric flavin oxidoreductase with a soluble 28 Kd PAS domain containing protein. PMID:26236298
Improving the Sequence Ontology terminology for genomic variant annotation. PMID:26229585
High-throughput sequencing of DNA G-quadruplex structures in the human genome. PMID:26192317
Inter-Individual Differences in the Oral Bacteriome Are Greater than Intra-Day Fluctuations in Individuals. PMID:26121551
LFQC: a lossless compression algorithm for FASTQ files. PMID:26093148
Combined Targeted DNA Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using UNCseq and NGScopy, and RNA Sequencing Using UNCqeR for the Detection of Genetic Aberrations in NSCLC. PMID:26076459
A parallel and sensitive software tool for methylation analysis on multicore platforms. PMID:26069264
RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application. PMID:26046471
Screening currency notes for microbial pathogens and antibiotic resistance genes using a shotgun metagenomic approach. PMID:26035208
HPV16 CpG methyl-haplotypes are associated with cervix precancer and cancer in the Guanacaste natural history study. PMID:26001326
PathoQC: Computationally Efficient Read Preprocessing and Quality Control for High-Throughput Sequencing Data Sets. PMID:25983538
MicroRNA transcriptome analysis identifies miR-365 as a novel negative regulator of cell proliferation in Zmpste24-deficient mouse embryonic fibroblasts. PMID:25983189
UrQt: an efficient software for the Unsupervised Quality trimming of NGS data. PMID:25924884
Identifying Human Genome-Wide CNV, LOH and UPD by Targeted Sequencing of Selected Regions. PMID:25919136
Differential expression of circulating microRNAs according to severity of colorectal neoplasia. PMID:25770825
De novo assembly and annotation of the Asian tiger mosquito (Aedes albopictus) repeatome with dnaPipeTE from raw genomic reads and comparative analysis with the yellow fever mosquito (Aedes aegypti). PMID:25767248
The contribution of cohesin-SA1 to gene expression and chromatin architecture in two murine tissues. PMID:25735743
FASTAptamer: A Bioinformatic Toolkit for High-throughput Sequence Analysis of Combinatorial Selections. PMID:25734917
Analytical workflow profiling gene expression in murine macrophages. PMID:25708305
Next-generation sequencing identifies deregulation of microRNAs involved in both innate and adaptive immune response in ALK+ ALCL. PMID:25688981
Improved detection of artifactual viral minority variants in high-throughput sequencing data. PMID:25657642
Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics. PMID:25600152
Are special read alignment strategies necessary and cost-effective when handling sequencing reads from patient-derived tumor xenografts? PMID:25539684
Somatic mosaicism in the human genome. PMID:25513881
An active immune defense with a minimal CRISPR (clustered regularly interspaced short palindromic repeats) RNA and without the Cas6 protein. PMID:25512373
Integrative workflows for metagenomic analysis. PMID:25478562
Compression of next-generation sequencing quality scores using memetic algorithm. PMID:25474747
Interaction between conjugative and retrotransposable elements in horizontal gene transfer. PMID:25474706
A review of software for analyzing molecular sequences. PMID:25421430
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. PMID:25410596
Rapid evaluation and quality control of next generation sequencing data with FaQCs. PMID:25408143
Cysteine protease and cystatin expression and activity during soybean nodule development and senescence. PMID:25404209
Evaluation of variant identification methods for whole genome sequencing data in dairy cattle. PMID:25361890
Identification of target-binding peptide motifs by high-throughput sequencing of phage-selected peptides. PMID:25348396
In-depth transcriptome analysis of the red swamp crayfish Procambarus clarkii. PMID:25338101
De novo transcriptome sequencing analysis and comparison of differentially expressed genes (DEGs) in Macrobrachium rosenbergii in China. PMID:25329319
SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing. PMID:25103311
A community-based resource for automatic exome variant-calling and annotation in Mendelian disorders. PMID:25078076
metaseq: a Python package for integrative genome-wide analysis reveals relationships between chromatin insulators and associated nuclear mRNA. PMID:25063299
Defining loci in restriction-based reduced representation genomic data from nonmodel species: sources of bias and diagnostics for optimal clustering. PMID:25057498
Computational methods for DNA copy-number analysis of tumors. PMID:25030933
Characterization of a proposed dichorhavirus associated with the citrus leprosis disease and analysis of the host response. PMID:25004279
An integrated SNP mining and utilization (ISMU) pipeline for next generation sequencing data. PMID:25003610
Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication. PMID:24987520
Trypanosoma brucei histone H1 inhibits RNA polymerase I transcription and is important for parasite fitness in vivo. PMID:24946224
OccuPeak: ChIP-Seq peak calling based on internal background modelling. PMID:24936875
Application of next generation sequencing to CEPH cell lines to discover variants associated with FDA approved chemotherapeutics. PMID:24924344
Characterization of HPV DNA methylation of contiguous CpG sites by bisulfite treatment and massively parallel sequencing-the FRAGMENT approach. PMID:24917876
Lack of association of KATNAL1 gene sequence variants and azoospermia in humans. PMID:24913027
AAV-mediated delivery of zinc finger nucleases targeting hepatitis B virus inhibits active replication. PMID:24827459
The miRNAome of the postpartum dairy cow liver in negative energy balance. PMID:24725334
Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. PMID:24722405
Next Generation Sequencing of miRNAs - Strategies, Resources and Methods. PMID:24710011
A framework phylogeny of the American oak clade based on sequenced RAD data. PMID:24705617
Multi-perspective quality control of Illumina exome sequencing data using QC3. PMID:24703969
The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. PMID:24682267
eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing. PMID:24593312
Identification of differentially expressed microRNAs in metastatic melanoma using next-generation sequencing technology. PMID:24573402
Environmental arsenic exposure and microbiota in induced sputum. PMID:24566055
MicroRNA regulation of bovine monocyte inflammatory and metabolic networks in an in vivo infection model. PMID:24470219
XS: a FASTQ read simulator. PMID:24433564
Very low-level heteroplasmy mtDNA variations are inherited in humans. PMID:24377867
An extensive evaluation of read trimming effects on Illumina NGS data analysis. PMID:24376861
Comparative study of exome copy number variation estimation tools using array comparative genomic hybridization as control. PMID:24303503
Compression of structured high-throughput sequencing data. PMID:24260313
Data compression for sequencing data. PMID:24252160
PEAR: a fast and accurate Illumina Paired-End reAd mergeR. PMID:24142950
NeSSM: a Next-generation Sequencing Simulator for Metagenomics. PMID:24124490
Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology. PMID:24109552
Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. PMID:24092820
An evaluation of allele frequency estimation accuracy using pooled sequencing data. PMID:24088264
POPBAM: Tools for Evolutionary Analysis of Short Read Sequence Alignments. PMID:24027417
The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus. PMID:23985341
An analysis of the molecular evolution of hepatitis B viral genotypes A/B/D using a Bayesian evolutionary method. PMID:23937671
Unraveling genomic variation from next generation sequencing data. PMID:23885890
WEP: a high-performance analysis pipeline for whole-exome data. PMID:23815231
The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability. PMID:23793381
QualComp: a new lossy compressor for quality scores based on rate distortion theory. PMID:23758828
Transcription profile of soybean-root-knot nematode interaction reveals a key role of phythormones in the resistance reaction. PMID:23663436
Sequencing platform and library preparation choices impact viral metagenomes. PMID:23663384
Characterization of human plasma-derived exosomal RNAs by deep sequencing. PMID:23663360
Transcriptome of the Lymantria dispar (gypsy moth) larval midgut in response to infection by Bacillus thuringiensis. PMID:23658687
DDBJ read annotation pipeline: a cloud computing-based pipeline for high-throughput analysis of next-generation sequencing data. PMID:23657089
Compression of FASTQ and SAM format sequencing data. PMID:23533605
Next generation sequencing reveals the expression of a unique miRNA profile in response to a gram-positive bacterial infection. PMID:23472090
CRISPR-Cas systems in the cyanobacterium Synechocystis sp. PCC6803 exhibit distinct processing pathways involving at least two Cas6 and a Cmr2 protein. PMID:23441196
Parallel evolutionary dynamics of adaptive diversification in Escherichia coli. PMID:23431270
BayesHammer: Bayesian clustering for error correction in single-cell sequencing. PMID:23368723
HTQC: a fast quality control toolkit for Illumina sequencing data. PMID:23363224
FUSIM: a software tool for simulating fusion transcripts. PMID:23323884
NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets. PMID:23314324
MAPI: a software framework for distributed biomedical applications. PMID:23311574
HLA typing from RNA-Seq sequence reads. PMID:23259685
Next generation sequencing in clinical medicine: Challenges and lessons for pathology and biomedical informatics. PMID:23248761
Technical considerations for reduced representation bisulfite sequencing with multiplexed libraries. PMID:23193365
Optimal reference sequence selection for genome assembly using minimum description length principle. PMID:23186305
The effect of strand bias in Illumina short-read sequencing data. PMID:23176052
Generation of artificial FASTQ files to evaluate the performance of next-generation sequencing pipelines. PMID:23152858
The genetic landscape of mutations in Burkitt lymphoma. PMID:23143597
MOCAT: a metagenomics assembly and gene prediction toolkit. PMID:23082188
NGC: lossless and lossy compression of aligned high-throughput sequencing data. PMID:23066097
Combining laser microdissection and RNA-seq to chart the transcriptional landscape of fungal development. PMID:23016559
Single nucleotide polymorphisms can create alternative polyadenylation signals and affect gene expression through loss of microRNA-regulation. PMID:22915998
Compression of next-generation sequencing reads aided by highly efficient de novo assembly. PMID:22904078
A beginners guide to SNP calling from high-throughput DNA-sequencing data. PMID:22886560
BioJava: an open-source framework for bioinformatics in 2012. PMID:22877863
SIMPLEX: cloud-enabled pipeline for the comprehensive analysis of exome sequencing data. PMID:22870267
Comprehensive microRNA profiling in B-cells of human centenarians by massively parallel sequencing. PMID:22846614
Fitness analyses of all possible point mutations for regions of genes in yeast. PMID:22722372
A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE. PMID:22685393
Transcriptome sequencing of and microarray development for a Helicoverpa zea cell line to investigate in vitro insect cell-baculovirus interactions. PMID:22629315
Exome sequencing generates high quality data in non-target regions. PMID:22607156
Assessment of metagenomic assembly using simulated next generation sequencing data. PMID:22384016
Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions. PMID:22355574
The limits of genome-wide methods for pharmacogenomic testing. PMID:22344246
GemSIM: general, error-model based simulator of next-generation sequencing data. PMID:22336055
PANDAseq: paired-end assembler for illumina sequences. PMID:22333067
NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PMID:22312429
Characterizing ncRNAs in Human Pathogenic Protists Using High-Throughput Sequencing Technology. PMID:22303390
MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets. PMID:22210894
Enrich: software for analysis of protein function by enrichment and depletion of variants. PMID:22006916
Inference of population mutation rate and detection of segregating sites from next-generation sequence data. PMID:21840859
SEED: efficient clustering of next-generation sequences. PMID:21810899
Sequence-specific error profile of Illumina sequencers. PMID:21576222
Composite transcriptome assembly of RNA-seq data in a sheep model for delayed bone healing. PMID:21435219
Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PMID:21408061
Flower: extracting information from pyrosequencing data. PMID:21330287
Comparative whole genome sequencing reveals phenotypic tRNA gene duplication in spontaneous Schizosaccharomyces pombe La mutants. PMID:21317186
SAMStat: monitoring biases in next generation sequencing data. PMID:21088025
The sequence read archive. PMID:21062823
Microbiome profiling by illumina sequencing of combinatorial sequence-tagged PCR products. PMID:21048977
SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. PMID:20875133
Using the Velvet de novo assembler for short-read sequencing technologies. PMID:20836074
BioRuby: bioinformatics software for the Ruby programming language. PMID:20739307
SEWAL: an open-source platform for next-generation sequence analysis and visualization. PMID:20693400
Next-generation sequencing techniques for eukaryotic microorganisms: sequencing-based solutions to biological problems. PMID:20601439
TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets. PMID:20573248
Manipulation of FASTQ data with Galaxy. PMID:20562416
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deoxyribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: FASTQ Sequence and Sequence Quality Format; FASTQ Sequence and Sequence Quality Format; DOI: https://doi.org/10.25504/FAIRsharing.r2ts5t; Last edited: April 27, 2021, 8:02 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
experimental measurement
metasource: Fairsharing.org
version: FAIRsharing.org: FASTQ Sequence and Sequence Quality Format; FASTQ Sequence and Sequence Quality Format; DOI: https://doi.org/10.25504/FAIRsharing.r2ts5t; Last edited: April 27, 2021, 8:02 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
polypeptide_region
metasource: Fairsharing.org
version: FAIRsharing.org: FASTQ Sequence and Sequence Quality Format; FASTQ Sequence and Sequence Quality Format; DOI: https://doi.org/10.25504/FAIRsharing.r2ts5t; Last edited: April 27, 2021, 8:02 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
Tags
More detailed information about this field from each metasource.
deoxyribonucleic acid
metasource: Fairsharing.orgversion: FAIRsharing.org: FASTQ Sequence and Sequence Quality Format; FASTQ Sequence and Sequence Quality Format; DOI: https://doi.org/10.25504/FAIRsharing.r2ts5t; Last edited: April 27, 2021, 8:02 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
experimental measurement
metasource: Fairsharing.orgversion: FAIRsharing.org: FASTQ Sequence and Sequence Quality Format; FASTQ Sequence and Sequence Quality Format; DOI: https://doi.org/10.25504/FAIRsharing.r2ts5t; Last edited: April 27, 2021, 8:02 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
polypeptide_region
metasource: Fairsharing.orgversion: FAIRsharing.org: FASTQ Sequence and Sequence Quality Format; FASTQ Sequence and Sequence Quality Format; DOI: https://doi.org/10.25504/FAIRsharing.r2ts5t; Last edited: April 27, 2021, 8:02 a.m.; Last accessed: Jan 03 2022 7:12 p.m.
dna experimental measurement polypeptide region
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