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@nathanhaigh
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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
@leffj
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leffj commented Jul 26, 2016

this should work: gzip -dc test.fq.gz | deinterleave_fastq.sh f.fastq r.fastq

@GlastonburyC
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Or in python:

r1 = open(r1.fastq,'w')
r2 = open(r2.fastq,'w')
[r1.write(line) if (i % 8 < 4) else r2.write(line) for i, line in enumerate(open('interleaved.fastq'))]
fastq_1.close()
fastq_2.close()


@rrohwer
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rrohwer commented Aug 16, 2017

I love this and I'd like to include it as part of my routine workflow. Could you please include a license or a comment line to indicate that this is OK with you (or what you're OK with)? Thanks!!

@mahmadza
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Awesome. I'm also using this. Thanks a lot!

@spongebob22
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I am having trouble getting the files to compress. I am running as:

gzip -dc test.fq.gz | deinterleave_fastq.sh f.fastq r.fastq compress

But my files are deleaving as fastq not fastq.gz. Should i be running as:

gzip -dc test.fq.gz | deinterleave_fastq.sh f.fastq.gz r.fastq.gz compress

@keiranmraine
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This is really handy, I'd make a minimal improvement to protect against the input process being terminated at the end of a valid record (by chance). Just the addition of the following near the start:

set -e
set -o pipefail

If overly cautious you could add a bit more tee and confirm the lines written to read_1 and read_2 are equal number (if not it's a good indicator that the file may not be well formed) and the sum is that of the input:

# tmpdir would be necessary for the count_* files
tee >(paste - - - - - - - -  | tee >(cut -f 1-4 | tr "\t" "\n" | tee >(wc -l > count_a)\
 | gzip -c > $1) | cut -f 5-8 | tr "\t" "\n" | tee >(wc -l > count_b)\
 | gzip -c > $2) | wc -l > count_all
# then some checking of  values

@a-kroh
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a-kroh commented Sep 6, 2018

Worked well and fast, but created 4 empty lines at the end of the de-interleaved files that interferred with downstream applications and had to be removed manually. Maybe something that can be fixed in a future version.
Took me a while to figure out the problem (error message of downstream application was cryptic), thus I though this might be useful for others to know.

@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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