Purdue University

Commands

• fasta_clipping_histogram.pl
• fasta_formatter
• fasta_nucleotide_changer
• fastq_masker
• fastq_quality_boxplot_graph.sh
• fastq_quality_converter
• fastq_quality_filter
• fastq_quality_trimmer
• fastq_to_fasta
• fastx_artifacts_filter
• fastx_barcode_splitter.pl
• fastx_clipper
• fastx_collapser
• fastx_nucleotide_distribution_graph.sh
• fastx_nucleotide_distribution_line_graph.sh
• fastx_quality_stats
• fastx_renamer
• fastx_reverse_complement
• fastx_trimmer
• fastx_uncollapser

Module

You can load the modules by:

module load biocontainers
module load fastx_toolkit

Example job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run FASTX-Toolkit on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=fastx_toolkit
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers fastx_toolkit