https://bioinformaticsonline.com/snippets/view/43296/commandline-for-paired-end-reads-simulation-with-bbmap? https://bioinformaticsonline.com/snippets/view/43296/commandline-for-paired-end-reads-simulation-with-bbmap Thu, 19 Aug 2021 10:30:41 -0500 https://bioinformaticsonline.com/snippets/view/43296/commandline-for-paired-end-reads-simulation-with-bbmap (JitMetaENV) ➜ mixedSample git:(main) ✗ /home/urbe/Tools/bbmap/randomreads.sh ref=mixed.fa out=reads_BBMAP250.fq paired interleaved reads=100k length=250 mininsert=400 maxinsert=600 gaussian java -ea -Xmx162129m -cp /home/urbe/Tools/bbmap/current/ align2.RandomReads3 build=1 ref=mixed.fa out=reads_BBMAP250.fq paired interleaved reads=100k length=250 mininsert=400 maxinsert=600 gaussian Executing align2.RandomReads3 [build=1, ref=mixed.fa, out=reads_BBMAP250.fq, paired, interleaved, reads=100k, length=250, mininsert=400, maxinsert=600, gaussian] Writing reference. Executing dna.FastaToChromArrays2 [mixed.fa, 1, writeinthread=false, genscaffoldinfo=true, retain, waitforwriting=false, gz=true, maxlen=536670912, writechroms=true, minscaf=1, midpad=500, nodisk=false] Set genScaffoldInfo=true Writing chunk 1 Waiting for writing to finish. Finished. snpRate=0.0, max=0, unique=true insRate=0.0, max=0, len=(0-0) delRate=0.0, max=0, len=(0-0) subRate=0.0, max=0, len=(0-0) nRate =0.0, max=0, len=(0-0) genome=1 PERFECT_READ_RATIO=0.0 ADD_ERRORS_FROM_QUALITY=true REPLACE_NOREF=false paired=true read length=250 reads=100000 insert size=400-600 Wrote reads_BBMAP250.fq Time: 5.722 seconds.]]> Jit