CRAM
CRAM is a sequencing read file format that is highly space efficient by using reference-based compression of sequence data and offers both lossless and lossy modes of compression. Building on early proof-of-principle for reference-based compression (Hsi-Yang Fritz, et al. (2011). Genome Res. 21:734-740), the CRAM format balances usability with compression efficiency.
Description
More detailed information about this field from each metasource.
CRAM is a sequencing read file format that is highly space efficient by using reference-based compression of sequence data and offers both lossless and lossy modes of compression. Building on early proof-of-principle for reference-based compression (Hsi-Yang Fritz, et al. (2011). Genome Res. 21:734-740), the CRAM format balances usability with compression efficiency.
metasource: Fairsharing.orgversion: None
Webpage:
https://www.sanger.ac.uk/science/tools/cramWebpage
More detailed information about this field from each metasource.
Publications:
Publications
More detailed information about this field from each metasource.
Efficient storage of high throughput DNA sequencing data using reference-based compression
PMID: 21245279
metasource: Fairsharing.org
version: None
The Scramble conversion tool
PMID: 24930138
metasource: Fairsharing.org
version: None
Publications
More detailed information about this field from each metasource.
Efficient storage of high throughput DNA sequencing data using reference-based compression
PMID: 21245279
metasource: Fairsharing.org
version: None
The Scramble conversion tool
PMID: 24930138
metasource: Fairsharing.org
version: None
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Efficient storage of high throughput DNA sequencing data using reference-based compression
PubMed citations: 123.
123 articles citing: Efficient storage of high throughput DNA sequencing data using reference-based compression
Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space. PMID:35199087
GA4GH: International policies and standards for data sharing across genomic research and healthcare. PMID:35072136
CRAM 3.1: Advances in the CRAM File Format. PMID:34999766
SamQL: a structured query language and filtering tool for the SAM/BAM file format. PMID:34600480
PIGG defines the Emm blood group system. PMID:34535746
Hamming-shifting graph of genomic short reads: Efficient construction and its application for compression. PMID:34280186
Refget: standardised access to reference sequences. PMID:34260694
FASTA/Q data compressors for MapReduce-Hadoop genomics: space and time savings made easy. PMID:33752596
Megadepth: efficient coverage quantification for BigWigs and BAMs. PMID:33693500
HTSlib: C library for reading/writing high-throughput sequencing data. PMID:33594436
Twelve years of SAMtools and BCFtools. PMID:33590861
Sharp Second-Order Pointwise Asymptotics for Lossless Compression with Side Information. PMID:33286477
Comparison of Compression-Based Measures with Application to the Evolution of Primate Genomes. PMID:33265483
Efficient DNA sequence compression with neural networks. PMID:33179040
Revealing Prognosis-Related Pathways at the Individual Level by a Comprehensive Analysis of Different Cancer Transcription Data. PMID:33138076
Practical guide for managing large-scale human genome data in research. PMID:33097812
IonCRAM: a reference-based compression tool for ion torrent sequence files. PMID:32907531
Chromatin binding of FOXA1 is promoted by LSD1-mediated demethylation in prostate cancer. PMID:32868907
Towards standardization guidelines for in silico approaches in personalized medicine. PMID:32827396
A systematic comparison of pharmacogene star allele calling bioinformatics algorithms: a focus on CYP2D6 genotyping. PMID:32789024
Practical estimation of cloud storage costs for clinical genomic data. PMID:32529017
Vertical lossless genomic data compression tools for assembled genomes: A systematic literature review. PMID:32453750
Genomic Sequencing Capacity, Data Retention, and Personal Access to Raw Data in Europe. PMID:32435258
How Can Law and Policy Advance Quality in Genomic Analysis and Interpretation for Clinical Care? PMID:32342785
Tximeta: Reference sequence checksums for provenance identification in RNA-seq. PMID:32097405
GABAC: an arithmetic coding solution for genomic data. PMID:31830243
svtools: population-scale analysis of structural variation. PMID:31218349
Mind the gap: resources required to receive, process and interpret research-returned whole genome data. PMID:31161416
Cram-JS: reference-based decompression in node and the browser. PMID:31099383
Genomic Analysis in the Age of Human Genome Sequencing. PMID:30901550
Tackling the Challenges of FASTQ Referential Compression. PMID:30792576
Alfred: interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing. PMID:30520945
TRCMGene: A two-step referential compression method for the efficient storage of genetic data. PMID:30395579
BdBG: a bucket-based method for compressing genome sequencing data with dynamic de Bruijn graphs. PMID:30364599
Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects. PMID:30279509
Review of applications of high-throughput sequencing in personalized medicine: barriers and facilitators of future progress in research and clinical application. PMID:30084865
The Terabase Search Engine: a large-scale relational database of short-read sequences. PMID:30052772
Crumble: reference free lossy compression of sequence quality values. PMID:29992288
Genomic big data hitting the storage bottleneck. PMID:29782620
Diversity of fungi associated with roots of Calanthe orchid species in Korea. PMID:29299843
CALQ: compression of quality values of aligned sequencing data. PMID:29186284
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species. PMID:29092050
GeneComp, a new reference-based compressor for SAM files. PMID:29046896
Traversing the k-mer Landscape of NGS Read Datasets for Quality Score Sparsification. PMID:28825060
Alignment of 1000 Genomes Project reads to reference assembly GRCh38. PMID:28531267
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. PMID:28396521
The RNASeq-er API-a gateway to systematically updated analysis of public RNA-seq data. PMID:28369191
LW-FQZip 2: a parallelized reference-based compression of FASTQ files. PMID:28320326
Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes. PMID:27986821
ascatNgs: Identifying Somatically Acquired Copy-Number Alterations from Whole-Genome Sequencing Data. PMID:27930809
cgpCaVEManWrapper: Simple Execution of CaVEMan in Order to Detect Somatic Single Nucleotide Variants in NGS Data. PMID:27930805
A privacy-preserving solution for compressed storage and selective retrieval of genomic data. PMID:27789525
Comparison of high-throughput sequencing data compression tools. PMID:27776113
A new algorithm for "the LCS problem" with application in compressing genome resequencing data. PMID:27556803
Towards precision medicine. PMID:27528417
Fourth Generation of Next-Generation Sequencing Technologies: Promise and Consequences. PMID:27406789
Boiler: lossy compression of RNA-seq alignments using coverage vectors. PMID:27298258
Recommendations on e-infrastructures for next-generation sequencing. PMID:27267963
VariantBam: filtering and profiling of next-generational sequencing data using region-specific rules. PMID:27153727
The challenges of big data. PMID:27147249
CARGO: effective format-free compressed storage of genomic information. PMID:27131376
Novel bioinformatic developments for exome sequencing. PMID:27075447
Compressive mapping for next-generation sequencing. PMID:27054987
The real cost of sequencing: scaling computation to keep pace with data generation. PMID:27009100
Effect of lossy compression of quality scores on variant calling. PMID:26966283
MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression. PMID:26895947
The European Bioinformatics Institute in 2016: Data growth and integration. PMID:26673705
The International Nucleotide Sequence Database Collaboration. PMID:26657633
Biological data sciences in genome research. PMID:26430150
Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph. PMID:26370285
elPrep: High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling. PMID:26182406
Big Data: Astronomical or Genomical? PMID:26151137
ERGC: an efficient referential genome compression algorithm. PMID:26139636
Compression of Large genomic datasets using COMRAD on Parallel Computing Platform. PMID:26124572
GDC 2: Compression of large collections of genomes. PMID:26108279
LFQC: a lossless compression algorithm for FASTQ files. PMID:26093148
Light-weight reference-based compression of FASTQ data. PMID:26051252
QVZ: lossy compression of quality values. PMID:26026138
Data-dependent bucketing improves reference-free compression of sequencing reads. PMID:25910696
Quality score compression improves genotyping accuracy. PMID:25748910
Extending reference assembly models. PMID:25651527
Reference-based compression of short-read sequences using path encoding. PMID:25649622
Streamlined Genome Sequence Compression using Distributed Source Coding. PMID:25520552
The Essential Component in DNA-Based Information Storage System: Robust Error-Tolerating Module. PMID:25414846
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. PMID:25410596
Aligned genomic data compression via improved modeling. PMID:25395305
Fast lossless compression via cascading Bloom filters. PMID:25252952
Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution. PMID:24958926
The Scramble conversion tool. PMID:24930138
Advances in genome studies in plants and animals. PMID:24626952
ENZYMAP: exploiting protein annotation for modeling and predicting EC number changes in UniProt/Swiss-Prot. PMID:24586563
XS: a FASTQ read simulator. PMID:24433564
HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads. PMID:24368726
SRComp: short read sequence compression using burstsort and Elias omega coding. PMID:24349065
DNA-COMPACT: DNA COMpression based on a pattern-aware contextual modeling technique. PMID:24282536
The European Bioinformatics Institute's data resources 2014. PMID:24271396
Compression of structured high-throughput sequencing data. PMID:24260313
Data compression for sequencing data. PMID:24252160
Human neuroimaging as a "Big Data" science. PMID:24113873
Short read alignment with populations of genomes. PMID:23813006
QualComp: a new lossy compressor for quality scores based on rate distortion theory. PMID:23758828
Using Genome Query Language to uncover genetic variation. PMID:23751181
Sequence squeeze: an open contest for sequence compression. PMID:23596984
Computational solutions for omics data. PMID:23594911
Existing and emerging technologies for tumor genomic profiling. PMID:23589546
The future of DNA sequence archiving. PMID:23587147
Compression of FASTQ and SAM format sequencing data. PMID:23533605
Facing growth in the European Nucleotide Archive. PMID:23203883
Adaptive efficient compression of genomes. PMID:23146997
NGC: lossless and lossy compression of aligned high-throughput sequencing data. PMID:23066097
SCALCE: boosting sequence compression algorithms using locally consistent encoding. PMID:23047557
Compression of next-generation sequencing reads aided by highly efficient de novo assembly. PMID:22904078
Compressive genomics. PMID:22781691
Metagenomics - a guide from sampling to data analysis. PMID:22587947
Genomics and privacy: implications of the new reality of closed data for the field. PMID:22144881
GReEn: a tool for efficient compression of genome resequencing data. PMID:22139935
Next-generation sequencing technologies and applications for human genetic history and forensics. PMID:22115430
Major submissions tool developments at the European Nucleotide Archive. PMID:22080548
The Sequence Read Archive: explosive growth of sequencing data. PMID:22009675
ReCoil - an algorithm for compression of extremely large datasets of dna data. PMID:21988957
Developing and implementing an institute-wide data sharing policy. PMID:21955348
The real cost of sequencing: higher than you think! PMID:21867570
SEED: efficient clustering of next-generation sequences. PMID:21810899 -
The Scramble conversion tool
PubMed citations: 16.
16 articles citing: The Scramble conversion tool
CRAM 3.1: Advances in the CRAM File Format. PMID:34999766
HTSlib: C library for reading/writing high-throughput sequencing data. PMID:33594436
Genozip - A Universal Extensible Genomic Data Compressor. PMID:33585897
IonCRAM: a reference-based compression tool for ion torrent sequence files. PMID:32907531
Genomic Sequencing Capacity, Data Retention, and Personal Access to Raw Data in Europe. PMID:32435258
GABAC: an arithmetic coding solution for genomic data. PMID:31830243
Mind the gap: resources required to receive, process and interpret research-returned whole genome data. PMID:31161416
Cram-JS: reference-based decompression in node and the browser. PMID:31099383
CALQ: compression of quality values of aligned sequencing data. PMID:29186284
GeneComp, a new reference-based compressor for SAM files. PMID:29046896
Comparison of high-throughput sequencing data compression tools. PMID:27776113
CARGO: effective format-free compressed storage of genomic information. PMID:27131376
Novel bioinformatic developments for exome sequencing. PMID:27075447
Sambamba: fast processing of NGS alignment formats. PMID:25697820
Reference-based compression of short-read sequences using path encoding. PMID:25649622
DeeZ: reference-based compression by local assembly. PMID:25357237
Tags:
Tags
More detailed information about this field from each metasource.
dna sequence data
metasource: Fairsharing.org
version: None
high throughput screening
metasource: Fairsharing.org
version: None
next generation dna sequencing
metasource: Fairsharing.org
version: None
rna sequencing
metasource: Fairsharing.org
version: None
Tags
More detailed information about this field from each metasource.
dna sequence data
metasource: Fairsharing.orgversion: None
high throughput screening
metasource: Fairsharing.orgversion: None
next generation dna sequencing
metasource: Fairsharing.orgversion: None
rna sequencing
metasource: Fairsharing.orgversion: None
dna sequences high throughput screening next generation dna sequencing rna sequence
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