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@nathanhaigh
Last active January 22, 2024 15:25
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deinterleave FASTQ files
#!/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
@zhenzhen3008
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zhenzhen3008 commented Sep 7, 2018

Exactly like a-kroh mentioned, somehow it generates empty lines at the end of each output file. When I run the Trimmomatic, it exits during the run. Since I saw the comments, it does not take me too long to figure out what happened. This deinterleave_fastq.sh is pretty handy, it would be great if this problem got fixed.
I used
$ egrep -v '^$' EMPTYLINE.fastq > NO_EMPTYLINE.fastq
to remove the empty lines.

@ugayujy
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ugayujy commented Jun 14, 2019

Pretty cool!
Thanks

@sinamajidian
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Thank you all.
I've edited it a bit:

cat input.fastq | paste - - - - - - - - | tee | cut -f 1-4 | tr "\t" "\n" | egrep -v '^$' > R1.fastq
cat input.fastq | paste - - - - - - - - | tee | cut -f 5-8 | tr "\t" "\n" | egrep -v '^$' > R2.fastq

@michaelsilverstein
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michaelsilverstein commented Jun 18, 2021

Thanks everyone! Here is how I have been deinterleaving an entire directory of compressed fastq.gz:
https://gist.github.com/michaelsilverstein/04c880b8e7728982ee57399599cfb56d#file-deinterleave_dir-sh

#!/bin/bash 

# Deinterleave entire directory of compressed .fastq.gz files and re-compress mates

#Usage: deinterleave_dir.sh indir outdir

mkdir $2

for file in $1/*
do
        echo $file
        out1=$2/$(basename ${file%.fastq.gz})_R1.fastq.gz
        out2=$2/$(basename ${file%.fastq.gz})_R2.fastq.gz
        pigz --best --processes 16 -dc $file | deinterleave_fastq.sh $out1 $out2 compress
done

This script will read compressed files from indir, deinterleave them, and save them to outdir with _R1.fastq.gz and _R2.fastq.gz file extensions.

@telatin
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telatin commented Oct 1, 2021

Hi! SeqFu bundles seqfu interleave and seqfu deinterleave. It's fast (compiled), and provides an easier and less error-prone CLI experience.
If you want to give a try see SeqFu website.

Can be installed via miniconda: conda install -c bioconda seqfu.

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