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[ 原始碼: kmc  ]

套件: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).

標籤: 領域: 生物學, 生物資訊學, 實做語言: implemented-in::c++, interface::commandline, 使用者介面: Command Shell, 角色: role::program, science::calculation, 範圍: 實用程式, Purpose: Analysing, Calculating

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下載可用於所有硬體架構的
硬體架構 套件大小 安裝後大小 檔案
alpha (非官方移植版) 465。1 kB2,511。0 kB [檔案列表]
amd64 454。6 kB2,101。0 kB [檔案列表]
arm64 417。3 kB1,869。0 kB [檔案列表]
armel 432。9 kB1,987。0 kB [檔案列表]
armhf 459。2 kB1,467。0 kB [檔案列表]
hppa (非官方移植版) 617。6 kB2,665。0 kB [檔案列表]
i386 527。9 kB2,627。0 kB [檔案列表]
m68k (非官方移植版) 511。1 kB2,543。0 kB [檔案列表]
mips 499。2 kB2,946。0 kB [檔案列表]
mips64el 402。6 kB2,619。0 kB [檔案列表]
mipsel 511。5 kB2,950。0 kB [檔案列表]
powerpcspe (非官方移植版) 522。5 kB2,600。0 kB [檔案列表]
ppc64 (非官方移植版) 441。2 kB2,665。0 kB [檔案列表]
ppc64el 466。9 kB2,537。0 kB [檔案列表]
riscv64 (非官方移植版) 445。6 kB1,583。0 kB [檔案列表]
s390x 402。1 kB2,189。0 kB [檔案列表]
sh4 (非官方移植版) 709。2 kB2,279。0 kB [檔案列表]
sparc64 (非官方移植版) 375。3 kB1,994。0 kB [檔案列表]
x32 (非官方移植版) 447。2 kB2,003。0 kB [檔案列表]