Fastx_toolkit

Introduction

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

For more information, please check:

BioContainers: https://biocontainers.pro/tools/fastx_toolkit

Home page: https://github.com/agordon/fastx_toolkit

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster	Version(s)
ANVIL	0.0.14
BELL	0.0.14
GAUTSCHI	0.0.14
NEGISHI	0.0.14
SCHOLAR	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:

Anvil

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition 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
module biocontainers fastx_toolkit

# Your fastx_toolkit workflow...

Bell, Gautschi, or Negishi

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers fastx_toolkit

# Your fastx_toolkit workflow...

Gautschi-AI

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers fastx_toolkit

# Your fastx_toolkit workflow...

Gilbreth

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers fastx_toolkit

# Your fastx_toolkit workflow...

Scholar

#!/bin/bash
#SBATCH -A queue     # Queue 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
module biocontainers fastx_toolkit

# Your fastx_toolkit workflow...