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annotate SeqSero2S/bin/deinterleave_fastq.sh @ 19:cfc91e1d2c9b draft

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planemo upload commit 936a627c4fc706080f07ec678f89e8256a7e7895
author jpayne
date Fri, 15 May 2026 17:50:45 +0000
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1 #!/bin/bash
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2 # Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress]
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3 #
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4 # Deinterleaves a FASTQ file of paired reads into two FASTQ
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5 # files specified on the command line. Optionally GZip compresses the output
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6 # FASTQ files using pigz if the 3rd command line argument is the word "compress"
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7 #
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8 # Can deinterleave 100 million paired reads (200 million total
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9 # reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s)
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10 #
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11 # Latest code: https://gist.github.com/3521724
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12 # Also see my interleaving script: https://gist.github.com/4544979
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13 #
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14 # Inspired by Torsten Seemann's blog post:
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15 # http://thegenomefactory.blogspot.com.au/2012/05/cool-use-of-unix-paste-with-ngs.html
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16
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17 # Set up some defaults
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18 GZIP_OUTPUT=0
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19 PIGZ_COMPRESSION_THREADS=10
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20
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21 # If the third argument is the word "compress" then we'll compress the output using pigz
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22 if [[ $3 == "compress" ]]; then
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23 GZIP_OUTPUT=1
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24 fi
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25
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26 if [[ ${GZIP_OUTPUT} == 0 ]]; then
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27 paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" > $1) | cut -f 5-8 | tr "\t" "\n" > $2
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28 else
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29 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
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30 fi