fastx_toolkit
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'fastx_toolkit' Versions
- 0.0.14
Link to section 'Commands' of 'fastx_toolkit' 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
Link to section 'Module' of 'fastx_toolkit' Module
You can load the modules by:
module load biocontainers
module load fastx_toolkit
Link to section 'Example job' of '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