Tuesday, October 30, 2012

How to make Bowtie read gziped files

Unlike Bowtie2,  Bowtie cannot read gzip files. So if you are not using Bowtie2, but Bowtie, use mkfifo so Bowtie can read gz files:

mkfifo file1.fifo
mkfifo file2.fifo
gunzip -c file1.gz > file1.fifo &
gunzip -c file2.gz > file2.fifo &
bowtie -1 file1.fifo -2 file2.fifo


  1. there's an issue with bowtie that can make this unreliable (it opens and reopens the file). you should use the patched version: https://github.com/earonesty/bowtie

  2. Is this still not fixed in the master versin?