Cdbtools

Introduction

Cdbtools is a collection of tools used for creating indices for quick retrieval of any particular sequences from large multi-FASTA files.

For more information, please check its website: https://biocontainers.pro/tools/cdbtools and its home page: http://compbio.dfci.harvard.edu/tgi.

Versions

• 0.99

Commands

• cdbfasta

• cdbyank

Module

You can load the modules by:

module load biocontainers
module load cdbtools

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 Cdbtools on our clusters:

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

module --force purge
ml biocontainers cdbtools

cdbfasta genome.fa
cdbyank -a 'seq_1' genome.fa.cidx