The BBMap package's reformat tool will do bam -> fastq conversion. I just tested it, and it ran at 50 Mbps/s, limited by Samtools conversion (it runs samtools in a subprocess for bam -> sam conversion). Sam.gz -> fastq is slightly faster at 70 Mbp/s. Converting a 2.5 GB sorted, mapped bam file took 88 seconds and produced a 10.5 GB fastq, so that's 120 MB/s for the raw fastq output. Gzipped fastq takes the same amount of time if you have pigz installed.

Usage:

reformat.sh in=reads.bam out=reads.fq primaryonly

4.7 years ago by


Ron

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