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

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 -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=trycycler
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load trycycler/XXXX ### you can run *module avail trycycler* to check all available versions

trycycler cluster --assemblies \
       test/test_cluster/assembly_*.fasta \
       --read test/test_cluster/reads.fastq \
       --out_dir trycycler_out