conda install -c bioconda bbmap
>/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 firstname.lastname@example.org 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