套件：kmc（3.2.4+dfsg-1 以及其他的）

[ 原始碼： kmc  ]

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

其他與 kmc 有關的套件

• dep: libbz2-1.0 [ia64, x32]

  high-quality block-sorting file compressor library - runtime

• dep: libc6 (>= 2.16) [x32]

  GNU C 函式庫：共用函式庫
  同時作為一個虛擬套件由這些套件填實： libc6-udeb

  dep: libc6 (>= 2.34) [除 alpha, ia64, sh4, x32]

  dep: libc6 (>= 2.37) [sh4]

• dep: libc6.1 (>= 2.31) [ia64]

  GNU C 函式庫：共用函式庫
  同時作為一個虛擬套件由這些套件填實： libc6.1-udeb

  dep: libc6.1 (>= 2.34) [alpha]

• dep: libgcc-s1 (>= 3.0) [amd64, arm64, mips64el, ppc64, ppc64el, s390x, x32]

  GCC 支援函式庫

  dep: libgcc-s1 (>= 3.4) [alpha]

  dep: libgcc-s1 (>= 3.5) [armel, armhf]

  dep: libgcc-s1 (>= 4.2) [i386, ia64, sh4]

  dep: libgcc-s1 (>= 4.3) [riscv64, sparc64]

• dep: libgcc-s2 (>= 4.2.1) [m68k]

  GCC 支援函式庫

• dep: libgcc-s4 (>= 4.1.1) [hppa]

  GCC 支援函式庫

• dep: libgomp1 (>= 4.9) [x32]

  GCC OpenMP (GOMP) support library

• dep: libstdc++6 (>= 13.1) [除 ia64, x32]

  GNU Standard C++ Library v3

  dep: libstdc++6 (>= 6) [ia64, x32]

• dep: libunwind8 [ia64]

  library to determine the call-chain of a program - runtime

• dep: zlib1g (>= 1:1.2.6)

  壓縮函式庫 - 跑程式時用(runtime)

下載 kmc

下載可用於所有硬體架構的

硬體架構	版本	套件大小	安裝後大小	檔案
alpha （非官方移植版）	3.2.4+dfsg-1	800。3 kB	4，403。0 kB	[檔案列表]
amd64	3.2.4+dfsg-1	991。7 kB	4，709。0 kB	[檔案列表]
arm64	3.2.4+dfsg-1	823。1 kB	4，013。0 kB	[檔案列表]
armel	3.2.4+dfsg-1	843。3 kB	4，024。0 kB	[檔案列表]
armhf	3.2.4+dfsg-1	880。0 kB	2，864。0 kB	[檔案列表]
hppa （非官方移植版）	3.2.4+dfsg-1	1，157。8 kB	4，715。0 kB	[檔案列表]
i386	3.2.4+dfsg-1	1，018。6 kB	4，884。0 kB	[檔案列表]
ia64 （非官方移植版）	3.1.1+dfsg-4	915。5 kB	8，074。0 kB	[檔案列表]
m68k （非官方移植版）	3.2.4+dfsg-1	962。0 kB	4，680。0 kB	[檔案列表]
mips64el	3.2.4+dfsg-1	739。6 kB	4，883。0 kB	[檔案列表]
ppc64 （非官方移植版）	3.2.4+dfsg-1	826。7 kB	5，037。0 kB	[檔案列表]
ppc64el	3.2.4+dfsg-1	904。2 kB	4，909。0 kB	[檔案列表]
riscv64	3.2.4+dfsg-1	901。4 kB	3，037。0 kB	[檔案列表]
s390x	3.2.4+dfsg-1	935。1 kB	4，621。0 kB	[檔案列表]
sh4 （非官方移植版）	3.2.4+dfsg-1	1，331。0 kB	4，267。0 kB	[檔案列表]
sparc64 （非官方移植版）	3.2.4+dfsg-1	690。0 kB	6，198。0 kB	[檔案列表]
x32 （非官方移植版）	2.3+dfsg-10	496。6 kB	2，254。0 kB	[檔案列表]