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[ Source: kmc  ]

Package: kmc (2.3+dfsg-7)

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count kmers in genomic sequences

The kmc software is designed for counting k-mers (sequences of consecutive k symbols) in a set of reads. K-mer counting is important for many bioinformatics applications, e.g. developing de Bruijn graph assemblers.

Building de Bruijn graphs is a commonly used approach for genome assembly with data from second-generation sequencing. Unfortunately, sequencing errors (frequent in practice) result in huge memory requirements for de Bruijn graphs, as well as long build time. One of the popular approaches to handle this problem is filtering the input reads in such a way that unique k-mers (very likely obtained as a result of an error) are discarded.

Thus, KMC scans the raw reads and produces a compact representation of all non-unique reads accompanied with number of their occurrences. The algorithm implemented in KMC makes use mostly of disk space rather than RAM, which allows one to use KMC even on rather typical personal computers. When run on high-end servers (what is necessary for KMC competitors) it outperforms them in both memory requirements and speed of computation. The disk space necessary for computation is in order of the size of input data (usually it is smaller).

Tags: Field: Biology, Bioinformatics, Implemented in: implemented-in::c++, interface::commandline, User Interface: Command Shell, Role: role::program, science::calculation, Scope: Utility, Purpose: Analysing, Calculating

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Download for all available architectures
Architecture Package Size Installed Size Files
amd64 454.6 kB2,101.0 kB [list of files]
arm64 417.3 kB1,869.0 kB [list of files]
armel 432.9 kB1,987.0 kB [list of files]
armhf 459.2 kB1,467.0 kB [list of files]
i386 527.9 kB2,627.0 kB [list of files]
mips 499.2 kB2,946.0 kB [list of files]
mips64el 402.6 kB2,619.0 kB [list of files]
mipsel 511.5 kB2,950.0 kB [list of files]
ppc64el 466.9 kB2,537.0 kB [list of files]
s390x 402.1 kB2,189.0 kB [list of files]