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photocyte/graphmap_streaming

Last active February 8, 2017 14:28
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graphmap_streaming
##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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