软件包：kmc（3.1.1+dfsg-3 以及其他的）

[ 源代码： 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).

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

其他与 kmc 有关的软件包

• dep: libbz2-1.0

  高品质块排序文件压缩程序库 - 运行时库

• dep: libc6 (>= 2.14) [amd64]

  GNU C 语言运行库：共享库
  同时作为一个虚包由这些包填实： libc6-udeb

  dep: libc6 (>= 2.17) [arm64, ppc64el]

  dep: libc6 (>= 2.4) [除 amd64, arm64, ppc64el]

• dep: libgcc-s1 (>= 3.0) [除 armel, armhf, i386, mipsel]

  GCC 支持库

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

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

• dep: libstdc++6 (>= 6)

  GNU 标准 C++ 库，第3版

• dep: zlib1g (>= 1:1.2.6)

  压缩库 - 运行时

下载 kmc

下载可用于所有硬件架构的

硬件架构	版本	软件包大小	安装后大小	文件
amd64	3.1.1+dfsg-3+b2	861.5 kB	3,954.0 kB	[文件列表]
arm64	3.1.1+dfsg-3+b2	672.7 kB	2,930.0 kB	[文件列表]
armel	3.1.1+dfsg-3+b2	712.5 kB	3,291.0 kB	[文件列表]
armhf	3.1.1+dfsg-3+b2	753.0 kB	2,355.0 kB	[文件列表]
i386	3.1.1+dfsg-3+b2	1,056.6 kB	5,287.0 kB	[文件列表]
mips64el	3.1.1+dfsg-3+b2	636.4 kB	3,919.0 kB	[文件列表]
mipsel	3.1.1+dfsg-3+b2	900.0 kB	4,681.0 kB	[文件列表]
ppc64el	3.1.1+dfsg-3+b2	744.2 kB	3,946.0 kB	[文件列表]
s390x	3.1.1+dfsg-3+b2	649.1 kB	3,554.0 kB	[文件列表]