macでインフォマティクス

macでインフォマティクス

NGS関連のインフォマティクス情報についてまとめています。

アダプタートリミングツール Skewer

 

Skewerは並列化に対応したアダプタートリミングツール。ミスマッチの閾値を設定し、それ以上の配列を全てトリミングするように設計されている。シングルエンド、ペアードエンド、ロングインサートのメイトペアのシーケンスリードを扱うことができる。Demultiplexingやindelを考慮したアダプター検出、phead quality scoreに応じたトリミングが可能になっている。

  

 

インストール

Github

git clone https://github.com/relipmoc/skewer.git 
cd skewer/
make
sudo make install #/user/local/bin/にバイナリがmoveされる。

skewer --help #動作確認

 user$ skewer --help

Skewer (A fast and accurate adapter trimmer for paired-end reads)

Version 0.2.2 (updated in April 4, 2016), Author: Hongshan Jiang

 

USAGE: skewer [options] <reads.fastq> [paired-reads.fastq]

    or skewer [options] - (for input from STDIN)

 

OPTIONS (ranges in brackets, defaults in parentheses):

 Adapter:

          -x <str> Adapter sequence/file (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)

          -y <str> Adapter sequence/file for pair-end reads (AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA),

                   implied by -x if -x is the only one specified explicitly.

          -M, --matrix <str> File indicates valid adapter pairing (all-ones matrix).

          -j <str> Junction adapter sequence/file for Nextera Mate Pair reads (CTGTCTCTTATACACATCTAGATGTGTATAAGAGACAG)

          -m, --mode <str> trimming mode; 1) single-end -- head: 5' end; tail: 3' end; any: anywhere (tail)

                           2) paired-end -- pe: paired-end; mp: mate-pair; ap: amplicon (pe)

          -b, --barcode    Demultiplex reads according to adapters/primers (no)

 Tolerance:

          -r <num> Maximum allowed error rate (normalized #errors / length of aligned region) [0, 0.5], (0.1)

          -d <num> Maximum allowed indel error rate [0, r], (0.03)

                   reciprocal is used for -r, -e and -d when num > or = 2

          -k <int> Minimum overlap length for adapter detection [1, inf);

                   (max(1, int(4-10*r)) for single-end; (<junction length>/2) for mate-pair)

 Clipping:

          -c, --cut <int>,<int> Hard clip off the 5' leading bases as the barcodes in amplicon mode; (no)

          -e, --cut3            Hard clip off the 3' tailing bases if the read length is greater than

                                the maximum read length specified by -L; (no)

 Filtering:

          -q, --end-quality  <int> Trim 3' end until specified or higher quality reached; (0)

          -Q, --mean-quality <int> The lowest mean quality value allowed before trimming; (0)

          -l, --min <int> The minimum read length allowed after trimming; (18)

          -L, --max <int> The maximum read length allowed after trimming; (no limit)

          -n  Whether to filter out highly degenerative (many Ns) reads; (no)

          -u  Whether to filter out undetermined mate-pair reads; (no)

          -N, --fillNs Whether to replace trimmed bases with Ns (has no effect with 'b' or '-m mp'); (no)

 Input/Output:

          -f, --format <str>   Format of FASTQ quality value: sanger|solexa|auto; (auto)

          -o, --output <str>   Base name of output file; ('<reads>.trimmed')

          -z, --compress       Compress output in GZIP format (no)

          -1, --stdout         Redirect output to STDOUT, suppressing -b, -o, and -z options (no)

          --qiime              Prepare the "barcodes.fastq" and "mapping_file.txt" for processing with QIIME; (default: no)

          --quiet              No progress update (not quiet)

          -A, --masked-output  Write output file(s) for trimmed reads (trimmed bases converted to lower case) (no)

          -X, --excluded-output Write output file(s) for excluded reads (no)

 Miscellaneous:

          -i, --intelligent     For mate-pair mode, whether to redistribute reads based on junction information; (no)

          -t, --threads <int>   Number of concurrent threads [1, 32]; (1)

 

EXAMPLES:

          skewer -Q 9 -t 2 -x adapters.fa sample.fastq -o trimmed

          skewer -x AGATCGGAAGAGC -q 3 sample-pair1.fq.gz sample-pair2.fq.gz

          skewer -x TCGTATGCCGTCTTCTGCTTGT -l 16 -L 30 -d 0 srna.fastq

          skewer -m mp -i lmp-pair1.fastq lmp-pair2.fastq

          skewer -m ap --cut 0,6 --qiime -x forward-primers.fa -y reverse-primers.fa mix-pair1.fastq mix-pair2.fastq

 

ラン

ペアリードのアダプター配列をトリミングする。

skewer -m pe -x AGATCGGAAGAGC -t 12 -l 18 sample-pair1.fq.gz sample-pair2.fq.gz -o trimmed
  • -x <str> Adapter sequence
  • -m <str> trimming mode; 1) single-end -- head: 5' end; tail: 3' end; any: anywhere (tail) 2) paired-end -- pe: paired-end; mp: mate-pair; ap: amplicon (pe)
  • -l <int> The minimum read length allowed after trimming; (18)
  • -t <int> Number of concurrent threads [1, 32]; (1)

 

 

 

 

 

引用

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.

Jiang H1, Lei R, Ding SW, Zhu S.

BMC Bioinformatics. 2014 Jun 12;15:182. doi: 10.1186/1471-2105-15-182.