CRAM protocols

CRAM specifications

Information


Unique identifier OMICS_00952
Name CRAM
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Input format FASTA
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 2.1
Stability Stable
Maintained Yes

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Publications for CRAM

CRAM IN pipelines

 (8)
2017
PMCID: 5522380
PMID: 28531267
DOI: 10.1093/gigascience/gix038

[…] [1]., as summarized in table 1, the alignment pipeline started with 63 744 gigabases of low-coverage sequence and 28 152 gigabases of wes sequence. the total amounts of aligned sequence in the final cram files are slightly larger—66 437 and 30 901 gigabases, respectively—because some of the reads are mapped to multiple locations such as the primary chromosomal region and its corresponding alt […]

2015
PMCID: 4504710
PMID: 26182406
DOI: 10.1371/journal.pone.0132868

[…] specific use cases., alignment and analysis tools communicate via sequence alignment/map (sam) files, a standardised file format for storing mapped reads [3], or the compressed variants thereof (bam/cram) [4, 5]. a sam file is a tab-separated file that stores information about the reads generated by the sequencer, such as their query template names and their segment sequences, as well […]

2013
PMCID: 3832420
PMID: 24260313
DOI: 10.1371/journal.pone.0079871

[…] but practical. another key weakness of the bam format is that bam files require approximately the same amount of storage as the unaligned reads, for each alignment represented in the format., the cram format, developed for the european nucleotide archive, was developed to try and compress hts alignments better than can be achieved with bam. cram achieves strong compression of alignment files […]

2013
PMCID: 3832420
PMID: 24260313
DOI: 10.1371/journal.pone.0079871

[…] for each alignment represented in the format., the cram format, developed for the european nucleotide archive, was developed to try and compress hts alignments better than can be achieved with bam. cram achieves strong compression of alignment files using custom developed compression approaches parameterized on characteristics of simulated hts alignment data [7]. a key innovation of cram […]

2013
PMCID: 3832420
PMID: 24260313
DOI: 10.1371/journal.pone.0079871

[…] with bam. cram achieves strong compression of alignment files using custom developed compression approaches parameterized on characteristics of simulated hts alignment data [7]. a key innovation of cram was the recognition that different applications need to preserve different subsets of the data contained in a bam file. preserving different subsets of the information can yield substantial […]

CRAM institution(s)
EMBL-Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK

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