Recycler

Introduction

Recycler is a tool designed for extracting circular sequences from de novo assembly graphs.

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

Versions

  • 0.7

Commands

  • make_fasta_from_fastg.py

  • get_simple_cycs.py

  • recycle.py

Module

You can load the modules by:

module load biocontainers
module load recycler

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 Recycler on our clusters:

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

module --force purge
ml biocontainers recycler

recycle.py -g test/assembly_graph.fastg \
    -k 55 -b test/test.sort.bam -i True