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| ##Abusing file descriptors to have graphmap stream/pipe the .sam output into samtools for filtering and compression to .bam | |
| /lab/solexa_weng/testtube/graphmap/bin/Linux-x64/graphmap align -r mito_reference.fasta -d raw_reads.fasta -P -o /dev/fd/3 3>&1 1>&2 | samtools view -b -h -F 4 > aligned_reads.bam |
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