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ABySS

Assembles the very large data sets produced by sequencing individual human genomes. ABySS is a parallelized sequence assembler. The primary innovation in ABySS is a distributed representation of a de Bruijn graph (DBG), which allows parallel computation of the assembly algorithm across a network of commodity computers. The ABySS algorithm proceeds in two stages. First, all possible substrings of length k (termed k-mers) are generated from the sequence reads. The k-mer data set is then processed to remove read errors and initial contigs are built. In the second stage, mate-pair information is used to extend contigs by resolving ambiguities in contig overlaps.

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ABySS classification

ABySS specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
C, C++, Perl, Shell (Bash)
License:
GNU General Public License version 3.0
Version:
2.0.2
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS
Parallelization:
MPI
Computer skills:
Advanced
Stability:
Stable
Wikipedia:
https://github.com/bcgsc/abyss/wiki

ABySS distribution

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ABySS support

Documentation

Maintainers

  • Inanc Birol <>
  • Anthony Raymond <>

Additional information

https://github.com/bcgsc/abyss#abyss

Credits

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Publications

Institution(s)

Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada

Funding source(s)

This work was supported by Genome Canada, Genome British Columbia, and the British Columbia Cancer Foundation.

Link to literature

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