recycler
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'recycler' Versions
- 0.7
Link to section 'Commands' of 'recycler' Commands
- make_fasta_from_fastg.py
- get_simple_cycs.py
- recycle.py
Link to section 'Module' of 'recycler' Module
You can load the modules by:
module load biocontainers
module load recycler
Link to section 'Example job' of 'recycler' 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 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