Trycycler

Introduction

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.

For more information, please check:
Docker hub: https://hub.docker.com/r/staphb/trycycler
Home page: https://github.com/rrwick/Trycycler

Versions

0.5.0
0.5.3
0.5.4

Commands

trycycler

Module

You can load the modules by:

module load biocontainers
module load trycycler

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 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