[bioinfo]Single-end readのデータをPair-endにする。

BBMapのbbfakereads.shを利用する。

BBMapのインスコ。condaで即。

conda install -c bioconda bbmap

bbfakereadsは絶対パスを打ち込んで使う。自分のホームフォルダにminicondaをインスコしている場合は、/home/username/miniconda3/bin/bbfakereads.sh

>/home/username/miniconda3/bin/bbfakereads.sh

Written by Brian Bushnell
Last modified February 17, 2015
Description: Generates fake read pairs from ends of contigs or single reads.
Usage: bbfakereads.sh in= out= out2=
Out2 is optional; if there is only one output file, it will be written interleaved.
Standard parameters:
ow=f (overwrite) Overwrites files that already exist.
zl=4 (ziplevel) Set compression level, 1 (low) to 9 (max).
fastawrap=100 Length of lines in fasta output.
tuc=f (touppercase) Change lowercase letters in reads to uppercase.
qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto.
qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input).
qfin=<.qual file> Read qualities from this qual file, for the reads coming from 'in='
qfout=<.qual file> Write qualities from this qual file, for the reads going to 'out='
qfout2=<.qual file> Write qualities from this qual file, for the reads coming from 'out2='
verifyinterleaved=f (vint) When true, checks a file to see if the names look paired. Prints an error message if not.
tossbrokenreads=f (tbr) Discard reads that have different numbers of bases and qualities. By default this will be detected and cause a crash.
Faking parameters:
length=250 Generate reads of this length.
minlength=1 Don't generate reads shorter than this.
overlap=0 If you set overlap, then reads will by variable length, overlapping by 'overlap' in the middle.
identifier=null (id) Output read names are prefixed with this.
addspace=t Set to false to omit the space before /1 and /2 of paired reads.
Java Parameters:
-Xmx This will set Java's memory usage, overriding autodetection.
-Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
The max is typically 85% of physical memory.
-eoom This flag will cause the process to exit if an
out-of-memory exception occurs. Requires Java 8u92+.
-da Disable assertions.
Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.

以下は実行例。400bpのSE readを50bp被らせてPE readとして出力。

bbfakereads.sh -Xmx100g in=input.fastq.gz out1=output1.fq out2=output2.fq length=250 ow=t