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Samcomp | Compression of FASTQ and SAM format sequencing data

An algorithm for compression of FASTQ files. Samcomp performs reference based compression but requires previously aligned data in the SAM format instead. The tool is compared against existing algorithms for both reference based compression (CRAM, Goby) and non-reference based compression (DSRC, BAM) and other recently published competition entries (Quip, SCALCE).

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Samcomp forum

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Samcomp classification

Samcomp specifications

Unique identifier:
OMICS_00968
Interface:
Command line interface
Input format:
SAM, BAM
Operating system:
Unix/Linux
License:
BSD 2-clause “Simplified” License
Stability:
Stable
Software type:
Package/Module
Restrictions to use:
None
Output format:
SAM, BAM
Programming languages:
C++
Computer skills:
Advanced
Maintained:
Yes

Samcomp distribution

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Samcomp support

Maintainer

  • James Bonfield <>

Credits

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Publications

Institution(s)

Wellcome Trust Sanger Institute, Cambridge, UK; Dell Inc, Round Rock, TX, USA

Funding source(s)

This work was supported by the Wellcome Trust [098051] and Dell Inc.

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