Fastq Validation - NBISweden/workshop-genome_assembly GitHub Wiki

FastQ Validation

Notes:

• https://github.com/alastair-droop/fqtools

Command:

#!/usr/bin/env bash

PATH="$PATH:/path/to/fqtools"
JOB=$SLURM_ARRAY_TASK_ID

DATA_DIR=/path/to/reads
FILES=( $DATA_DIR/*_R1.fastq.gz )

FASTQ="${FILES[$JOB]}"
fqtools validate "$FASTQ" 
fqtools validate "${FASTQ/_R1./_R2.}"