jpayne@17: #!/bin/bash
jpayne@17: # Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress]
jpayne@17: # 
jpayne@17: # Deinterleaves a FASTQ file of paired reads into two FASTQ
jpayne@17: # files specified on the command line. Optionally GZip compresses the output
jpayne@17: # FASTQ files using pigz if the 3rd command line argument is the word "compress"
jpayne@17: # 
jpayne@17: # Can deinterleave 100 million paired reads (200 million total
jpayne@17: # reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s)
jpayne@17: # 
jpayne@17: # Latest code: https://gist.github.com/3521724
jpayne@17: # Also see my interleaving script: https://gist.github.com/4544979
jpayne@17: # 
jpayne@17: # Inspired by Torsten Seemann's blog post:
jpayne@17: # http://thegenomefactory.blogspot.com.au/2012/05/cool-use-of-unix-paste-with-ngs.html
jpayne@17: 
jpayne@17: # Set up some defaults
jpayne@17: GZIP_OUTPUT=0
jpayne@17: PIGZ_COMPRESSION_THREADS=10
jpayne@17: 
jpayne@17: # If the third argument is the word "compress" then we'll compress the output using pigz
jpayne@17: if [[ $3 == "compress" ]]; then
jpayne@17:   GZIP_OUTPUT=1
jpayne@17: fi
jpayne@17: 
jpayne@17: if [[ ${GZIP_OUTPUT} == 0 ]]; then
jpayne@17:   paste - - - - - - - -  | tee >(cut -f 1-4 | tr "\t" "\n" > $1) | cut -f 5-8 | tr "\t" "\n" > $2
jpayne@17: else
jpayne@17:   paste - - - - - - - -  | tee >(cut -f 1-4 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $1) | cut -f 5-8 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $2
jpayne@17: fi