Mercurial > repos > jpayne > seqsero_v2
view SeqSero2/deinterleave_fastq.sh @ 3:b18e8cdfdf81
planemo upload
author | jpayne |
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date | Tue, 13 Nov 2018 16:18:17 -0500 (2018-11-13) |
parents | fae43708974d |
children |
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#!/bin/bash # Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress] # # Deinterleaves a FASTQ file of paired reads into two FASTQ # files specified on the command line. Optionally GZip compresses the output # FASTQ files using pigz if the 3rd command line argument is the word "compress" # # Can deinterleave 100 million paired reads (200 million total # reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s) # # Latest code: https://gist.github.com/3521724 # Also see my interleaving script: https://gist.github.com/4544979 # # Inspired by Torsten Seemann's blog post: # http://thegenomefactory.blogspot.com.au/2012/05/cool-use-of-unix-paste-with-ngs.html # Set up some defaults GZIP_OUTPUT=0 PIGZ_COMPRESSION_THREADS=10 # If the third argument is the word "compress" then we'll compress the output using pigz if [[ $3 == "compress" ]]; then GZIP_OUTPUT=1 fi if [[ ${GZIP_OUTPUT} == 0 ]]; then paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" > $1) | cut -f 5-8 | tr "\t" "\n" > $2 else 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 fi