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[ 源代码: kmc  ]

软件包: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).

标签: 领域: 生物学, 生物信息学, 实做语言: implemented-in::c++, interface::commandline, 用户接口: Command Shell, 角色: role::program, science::calculation, 范围: 实用程序, Purpose: Analysing, 分布式计算

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下载可用于所有硬件架构的
硬件架构 软件包大小 安装后大小 文件
amd64 454.6 kB2,101.0 kB [文件列表]
arm64 417.3 kB1,869.0 kB [文件列表]
armel 432.9 kB1,987.0 kB [文件列表]
armhf 459.2 kB1,467.0 kB [文件列表]
i386 527.9 kB2,627.0 kB [文件列表]
mips 499.2 kB2,946.0 kB [文件列表]
mips64el 402.6 kB2,619.0 kB [文件列表]
mipsel 511.5 kB2,950.0 kB [文件列表]
ppc64el 466.9 kB2,537.0 kB [文件列表]
s390x 402.1 kB2,189.0 kB [文件列表]