QuorUMはMaSuRCAなどにも組み込まれているエラーコレクションパイプライン。
インストール
https://github.com/gmarcais/Quorum
brewで導入できる( macではエラーになったのでubuntu14.4にlinuxbrewで入れた)。
> quorum --help
user$ quorum --help
/home/linuxbrew/.linuxbrew/bin/quorum [options] .fastq [.fastq]+
Run the quorum error corrector on the given fastq file.
Options:
-s, --size Mer database size (default 200M)
-t, --threads Number of threads (default number of cpus)
-p, --prefix Output prefix (default quorum_corrected)
-k, --kmer-len Kmer length (default 24)
-q, --min-q-char Minimum quality char. Usually 33 or 64 (autodetect)
-m, --min-quality Minimum above -q for high quality base (5)
-w, --window Window size for trimming
-e, --error Maximum number of errors in a window
--min-count Minimum count for a k-mer to be good
--skip Number of bases to skip to find anchor kmer
--anchor Numer of good kmer in a row for anchor
--anchor-count Minimum count for an anchor kmer
--contaminant Contaminant sequences
--contaminant-trim Trim sequences with contaminant mers
--h-bash: nts$: command not found
実行方法
quorum -s 50M -t 12 -k 24 -q 33 input1.fq input2.fq -p output
- -s Mer database size (default 200M)
- -t Number of threads (default number of cpus)
- -p Output prefix (default quorum_corrected)
- -k Kmer length (default 24)
- -q Minimum quality char. Usually 33 or 64 (autodetect)
エラー補正されたfastqとmerファイルが出力される。
引用
QuorUM: An Error Corrector for Illumina Reads
Marçais G, Yorke JA, Zimin A
PLoS One. 2015 Jun 17;10(6):e0130821.
