This function automates FASTQ downsampling with seqtk, which can be easily parallelized with GNU parallel

downsample_fastq.sh

#!/bin/bash

downsample_fastq() {
    local input_fastq=$1  #$ FASTQ in .gz compression (ID_1.fastq.gz)
    local downsample_factor=$2
    
    local base_name=$(basename "$input_fastq" .fastq.gz)
    local prefix="${base_name%%_*}"
    local suffix="${base_name#*_}"
    local output_fastq="${prefix}s_${suffix}.fastq.gz"  # Add an "s" to the ID

    seqtk sample -s12 "$input_fastq" "$downsample_factor" | pigz > "$output_fastq"
    
    echo "Output file: $output_fastq"
}

export -f downsample_fastq

# Parallelize the function using GNU parallel
# parallel downsample_fastq ::: ID_1.fastq.gz ID_2.fastq.gz ::: 0.01