Software: trycycler
Description
Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes. I.e. if you have multiple long-read assemblies for the same isolate, Trycycler can combine them into a single assembly that is better than any of your inputs.
Available Versions
| Unspecified: | 0.5.0 0.5.3 0.5.4 |
|---|
Docker hub: https://hub.docker.com/r/staphb/trycycler
Home page: https://github.com/rrwick/Trycycler
Commands
- trycycler
Module
You can load the modules by:
module load biocontainers
module load trycycler
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
To run trycycler on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=trycycler
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers trycycler
trycycler cluster --assemblies \
test/test_cluster/assembly_*.fasta \
--read test/test_cluster/reads.fastq \
--out_dir trycycler_out