Add gzip/gunzip support to a program that doesn't have it (e.g. bowtie)

Keeping your FASTQ read files in gzip compressed format saves much of the precious space of you hard drives. Unfortunately, there are still some tools that do not support direct use of compressed files. For many tools, the following trick will work.

mkfifo mate1.fastq
mkfifo mate2.fastq
gunzip -c mate1.fastq.gz > mate1.fastq &
gunzip -c mate2.fastq.gz > mate2.fastq &
bowtie -S genome -1 mate1.fastq -2 mate2.fastq > sample.sam

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Last updated on May 06, 2013

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