アダプターやプライマーのコンタミを除く AlienTrimmer

シーケンスされる長さより短いライブラリサイズのシーケンスを行うと、3'側にアダプタやバーコードが出現する。このような汚染配列があると、後の解析に悪影響を与える可能性があるため、クオリティチェックの時に除くのが望ましい。AlienTrimmerはユーザが指定したk-merサイズに配列を分解し、汚染配列があるかどうか短時間で検出する。

マニュアルPDF

解凍したツール内にある。

インストール

FTPサイト

ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/

ダウンロードしたAlienTrimmer_0.4.0.tar.gzを解凍し、srcに入る。

chmod a+x JarMaker.sh 
./JarMaker.sh

java -jar AlienTrimmer.jar  #動作確認

user$ java -jar AlienTrimmer.jar

AlienTrimmer v.0.4.0

USAGE: AlienTrimmer [options]

Fast trimming to filter out non-confident nucleotides and alien oligo-

nucleotide sequences (adaptors, primers) in both 5' and 3' read ends

OPTIONS:

-i <infile> [single-ends] FASTQ formatted input file name

-if <infile> [paired-ends] FASTQ formatted input file name containing

forward (fwd) reads

-ir <infile> [paired-ends] FASTQ formatted input file name containing

reverse (rev) reads

-o <outfile> [single-ends] output file name

-of <outfile> [paired-ends] output file name for trimmed fwd reads

-or <outfile> [paired-ends] output file name for trimmed rev reads

-os <outfile> [paired-ends] output file name for remaining trimmed

single (sgl) reads

-c [0-9]* [single-ends] alien sequence id(s) (see option -d)

-d [0-9] displays alien sequences for the specified id:

0: Homopolymers

1: Dimers

2: Trimers

-c <infile> [single-ends] input file name containing user-defined

alien sequence(s) (one line per sequence)

-cf [0-9]* [paired-ends] same as -c for only fwd reads

-cf <infile> [paired-ends] same as -c for only fwd reads

-cr [0-9]* [paired-ends] same as -c for only rev reads

-cr <infile> [paired-ends] same as -c for only rev reads

-k [5-15] k value for k-mer decomposition; must lie between 5 and

15 (default: k=10)

-m <int> allowed mismatch value (default: m=k/2)

-l <int> minimum read length to output; all trimmed reads with

length below this value are filtered out (default: l=15)

-q [0-40] Phred quality score cutoff to trim off low-quality read

ends; must lie between 0 and 20 (default: q=20)

-p [0-100] minimum allowed percentage of correctly called

nucleotides (i.e. with Phred quality score character

higher than q); all reads with a percentage of correctly

called nucleotide lower than this value are filtered out

(default: p=0)

-v displays trimming details during the whole process

EXAMPLES:

[single-ends]

AlienTrimmer -i reads.fq -o trim.fq -c 0 -l 30 -p 80

AlienTrimmer -i reads.fq -c aliens.fa -k 9 -q 10

[paired-ends]

AlienTrimmer -if fwd.fq -ir rev.fq -c alien.fa -q 0 -p 75

AlienTrimmer -if fwd.fq -ir rev.fq -cf alien.fwd.fa -cr alien.rev.fa

実行方法

汚染配列を指定してラン。

java -jar AlienTrimmer.jar -if fwd.fq -ir rev.fq -c alien.fa -q 0 -p 75

-if <infile>　[paired-ends] FASTQ formatted input file name containing forward (fwd) reads
-ir <infile>　[paired-ends] FASTQ formatted input file name containing reverse (rev) reads
-o <outfile>　[single-ends] output file name
-q [0-40]　Phred quality score cutoff to trim off low-quality read ends; must lie between 0 and 20 (default: q=20)
-p [0-100]　minimum allowed percentage of correctly called nucleotides (i.e. with Phred quality score character higher than q); all reads with a percentage of correctly called nucleotide lower than this value are filtered out (default: p=0)
-v　displays trimming details during the whole process