Originally posted by sk8bro
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BBMap is always nondeterministic when run in paired-end mode with multiple threads, because the insert-size average is calculated on a per-thread basis, which affects mapping; and which reads are assigned to which thread is nondeterministic. The only way to avoid that would be to restrict it to a single thread (threads=1), or map the reads as single-ended and then fix pairing afterward:
Code:
bbmap.sh in=reads.fq outu=unmapped.fq int=f repair.sh in=unmapped.fq out=paired.fq fint outs=singletons.fq
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