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Commandline for paired end reads simulation with BBMap !
By Jit 1226 days ago
(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.
