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