Deinterleave MGI FASTQ lanes

deinterleave_mgi_lanes.sh

#!/bin/bash
# This script deinterleaves a FASTQ file generated by an MGI sequencer with two flowcell lanes
# where headers are in the format: @v300009551L1C002R003000000/1 with L1 or L2 indicating the lane
# This can be useful for some analyses since each lane can behave like a technical replicate (eg DADA2 error correction?)

set -e
set -o pipefail

input_fastq_gz="$1"  # input FASTQ file
samplename="$(basename $input_fastq_gz .fastq.gz)"

lane1_file="${samplename}_lane1.fastq"
lane2_file="${samplename}_lane2.fastq"

# Use zcat to uncompress gz file, use awk to de-interleave
zcat "$input_fastq_gz" | awk -v l1="$lane1_file" -v l2="$lane2_file" 'BEGIN {FS="\n"; OFS="\n"}
    {
        header = $0;
        getline seq;
        getline plus;
        getline qual;
        if (header ~ /L1C/) 
            print header, seq, plus, qual > l1
        else if (header ~ /L2C/) 
            print header, seq, plus, qual > l2
    }'

# Compress the de-interleaved FASTQ files
gzip ${samplename}_lane1.fastq
gzip ${samplename}_lane2.fastq

test.fastq

@v300009551L1C002R003000000/1
AAGGCTCTCTACGACAGGGTTTACTACGTTAGCTGAT
+
III9IG9ICBGIH>FBGGIIGII;>=FBB9D:9?=BC;
@v300009551L2C002R003000001/1
AGCTACTGAGTCCGATGCATGCTAGCTAGCTGATGAC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@v300009551L1C002R003000002/1
GCGTAAGCTACGGTACGTTACGTTACGTGCGTGGTGGT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@v300009551L2C002R003000003/1
TGCTAGCTGACGATCGTAGCTGATGCTAGCTAGCTGAT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII