DemuxFastqs with multiple FASTQs per sub-read

concatenate_subread_fastqs.sh

#!/bin/bash

set -euo pipefail

# Concatenate the FASTQs per sub-read prior to running DemuxFastqs
cat SAMPLE1_S1_L001_R1_001.fastq.gz SAMPLE1_S1_L001_R1_002.fastq.gz > SAMPLE1_S1_L001_R1_COMBINED.fastq.gz;
cat SAMPLE1_S1_L001_R2_001.fastq.gz SAMPLE1_S1_L001_R2_002.fastq.gz > SAMPLE1_S1_L001_R2_COMBINED.fastq.gz;

# Run Demux Fastqs (try `conda install -c bioconda fgbio` to install `fgbio`).
# Note: since we have two sub-reads, we must have two read structures.
fgbio DemuxFastqs \
    -i SAMPLE1_S1_L001_R1_COMBINED.fastq.gz SAMPLE1_S1_L001_R2_COMBINED.fastq.gz
    -r 8B+T 8B+T \
    ...<other options>;

concatenate_subread_fastqs_on_the_fly.sh

#!/bin/bash

set -euo pipefail

# Run Demux Fastqs (try `conda install -c bioconda fgbio` to install `fgbio`).
# Note: since we have two sub-reads, we must have two read structures.
fgbio DemuxFastqs \
    -i <(cat SAMPLE1_S1_L001_R1_001.fastq.gz SAMPLE1_S1_L001_R1_002.fastq.gz) \
       <(cat SAMPLE1_S1_L001_R2_001.fastq.gz SAMPLE1_S1_L001_R2_002.fastq.gz) \
    -r 8B+T 8B+T \
    ...<other options>;