cram file to bam file
What is SAM BAM CRAM format?
SAM stands for Sequence Alignment Map and is described in the standard specification here.
BAM and CRAM are both compressed forms of SAM; BAM (for Binary Alignment Map) is a lossless compression while CRAM can range from lossless to lossy depending on how much compression you want to achieve (up to very much indeed).2 mai 2023CRAM files typically vary from 30 to 60% smaller than BAM, depending on the data held within them.
Implementations of CRAM exist in htsjdk, htslib, JBrowse, and Scramble.
What is the difference between BAM and CRAM?
BAM is a standard alignment format which was defined by the 1000 Genomes consortium and has since seen wide community adoption, whereas CRAM is a compressed version of this.
This compression is driven by the reference the sequence data is aligned to.
What is a .CRAM file?
CRAM is a more highly compressed alternative to the BAM and SAM DNA sequence alignment file formats.
CRAM is a format designed by the European Bioinformatics Institute.
It uses reference based compression, meaning that only base calls that differ to a designated reference sequence need to be stored.
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Sequence Alignment/Map Format Specification
22 août 2022 Each SAM and BAM file may optionally specify the version being used via the @HD VN tag. For full version history see Appendix B. Unless ... |
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CRAM 3.1: Advances in the CRAM Format
15 sept. 2021 Motivation: CRAM has established itself as a high compression alternative to the BAM file format for. DNA sequencing data. |
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Exome and Genome Sequencing Data
A CRAM file is a compressed BAM file. BAM files are the industry- standard format for storing aligned sequence data. Each CRAM file. |
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Genozip 14 - advances in compression of BAM and CRAM files
14 sept. 2022 Genozip performs compression of a wide range of genomic data including widely used. FASTQ |
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CRAM format specification (version 2.1)
Effortless transition to CRAM from using BAM files Pic.1 CRAM file starts with a file definition followed by the BAM header and other containers. |
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Genozip 14 - advances in compression of BAM and CRAM files
14 sept. 2022 Abstract. Summary. Genozip performs compression of a wide range of genomic data including widely used. FASTQ |
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CRAM format specification (version 3.0)
15 août 2022 Significantly better lossless compression than BAM. 2. Full compatibility with BAM. 3. Effortless transition to CRAM from using BAM files. |
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Bedtools Documentation
26 mai 2022 genome associated with your CRAM file via the CRAM_REFERENCE ... With the exception of BAM files bedtools assumes all input files are TAB ... |
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CRAM 3.1: advances in the CRAM file format
6 janv. 2022 Motivation: CRAM has established itself as a high compression alternative to the BAM file format for DNA sequenc- ing data. |
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Sam2lca: Lowest Common Ancestor for SAM/BAM/CRAM alignment
1 juin 2022 SAM/BAM/CRAM alignment files ... reference sequence accessions present in the BAM file header section |
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CRAM format specification (version 30) - Samtools
4 fév 2021 · Significantly better lossless compression than BAM 2 Full compatibility with BAM 3 Effortless transition to CRAM from using BAM files 4 |
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CRAM format specification (version 21) - Samtools
Effortless transition to CRAM from using BAM files 4 Support for Pic 1 CRAM file starts with a file definition followed by the BAM header and other containers |
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CRAM format specification version: 101 license - EMBL-EBI
Effortless transition to CRAM from using BAM files 4 Support for CRAM file format starts with a fixed length file definition followed by containers The first |
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Lossy Compression of Quality Values in Next-Generation - CORE
3 4 4 The CRAM format is a new format designed by the European Bioinformatics Insti- tute that compresses SAM/BAM files and achieves 40-50 space saving |
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The Scramble Conversion Tool - bioRxiv
28 mar 2014 · Motivation: The reference CRAM file format implementation is in Java We present “Scramble”: a new C implementation of SAM, BAM |
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HTSlib - bioRxiv
16 déc 2020 · It was born out of the widely used SAMtools and BCFtools applications protocols, the addition of the CRAM file format, better indexing and |
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NEXT-GENERATION SEQUENCING DATA - Dell Technologies
compresses FASTQ, BAM, and CRAM files The user-mode library, BAM File Compression Using PetaSuite Lossless Mode SAMPLE FILES ORIGINAL |
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Twelve years of SAMtools and BCFtools - Oxford Academic Journals
18 jan 2021 · There- fore in practice, the binary counterparts BAM or CRAM are used for alignment data and, when parsing of large VCF files becomes |
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Accelerating Data-Intensive Genome Analysis in the Cloud
verting the CRAM file to a lossless BAM file for downstream analysis in the cloud • To improve I/O performance, SeqInCloud intel- ligently maps input and output |
