FASTX-Toolkit

Introduction

FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

For more information, please check its website: https://biocontainers.pro/tools/fastx_toolkit and its home page on Github.

Versions

  • 0.0.14

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

Warning

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