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CRAM specifications


Unique identifier OMICS_00952
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


No version available

Publications for CRAM

CRAM citations


The European Nucleotide Archive in 2017

Nucleic Acids Res
PMCID: 5753375
PMID: 29140475
DOI: 10.1093/nar/gkx1125

[…] als ( ENA content spans raw read data from a variety of platforms and derived from over 3 million libraries, served in FASTQ and, where provided, CRAM formats; around 500 000 read alignments and re-alignments; levels of assembly from contigs through to completed closed chromosome (over 140 000 assemblies); approaching 900 million assembled/anno […]


Ensembl Genomes 2018: an integrated omics infrastructure for non vertebrate species

Nucleic Acids Res
PMCID: 5753204
PMID: 29092050
DOI: 10.1093/nar/gkx1011

[…] loped a pipeline to automatically identify sequence read data in the INSDC archives and align them to the corresponding genomic sequence. These alignments are stored in Compressed Read Alignment Map (CRAM) format () and are resubmitted to the ENA for persistent archiving. Data from technical replicates are merged by default. To make these thousands of tracks accessible in Ensembl Genomes, alignmen […]


Alignment of 1000 Genomes Project reads to reference assembly GRCh38

PMCID: 5522380
PMID: 28531267
DOI: 10.1093/gigascience/gix038

[…] All CRAM files supporting the results of this article are available in ENA and assigned accessions at both study and file levels. Study ERP013771 is the low-coverage WGS data set, which contains 2691 anal […]


The RNASeq er API—a gateway to systematically updated analysis of public RNA seq data

PMCID: 5870697
PMID: 28369191
DOI: 10.1093/bioinformatics/btx143
call_split See protocol

[…] for the wheat genome reference, but now that TopHat 2 has been improved to handle large genome references, we plan to use TopHat 2 only for all species. Then the resulting BAM () file is converted to CRAM () format; bigWig ( and bedGraph ( genome track files are also generated. Where groups of […]


Novel bioinformatic developments for exome sequencing

Hum Genet
PMCID: 4883269
PMID: 27075447
DOI: 10.1007/s00439-016-1658-6

[…] / The CRAM format is now supported by some widely used genomic analysis tools such as SAMtools, Picard and GATK (Li et al. ; McKenna et al. ). With the increasing support for the CRAM format, it may well replace the use of BAM files in the near future.With ever growing datasets containing variants of thousands of individuals, it becomes worthwhile to compress the relatively sm […]


The International Nucleotide Sequence Database Collaboration

Nucleic Acids Res
PMCID: 4702924
PMID: 26657633
DOI: 10.1093/nar/gkv1323

[…] le this rate is slower than in previous years, it remains rapid and challenging in terms of managing network and data storage.INSDC partners continue to exploit reference-based compression models (). CRAM ( and cSRA ( are supported in sequence databases at EMBL-EBI and NCBI, respectively. In a […]


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

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