パッケージ: kmc (2.3+dfsg-7)
kmc に関するリンク
Debian の資源:
kmc ソースパッケージをダウンロード:
メンテナ:
- Debian Med Packaging Team (QA ページ, メールアーカイブ)
- Andreas Tille (QA ページ)
- Jorge Soares (QA ページ)
- Sascha Steinbiss (QA ページ)
- Kevin Murray (QA ページ)
外部の資源:
- ホームページ [sun.aei.polsl.pl]
類似のパッケージ:
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).
その他の kmc 関連パッケージ
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