Deepconsensus

Introduction

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.

For more information, please check:
Docker hub: https://hub.docker.com/r/google/deepconsensus
Home page: https://github.com/google/deepconsensus

Versions

0.2.0

Commands

deepconsensus
ccs
actc

Module

You can load the modules by:

module load biocontainers
module load deepconsensus

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 deepconsensus on our clusters:

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

module --force purge
ml biocontainers deepconsensus

deepconsensus run \
    --subreads_to_ccs=subreads_to_ccs.bam  \
    --ccs_fasta=ccs.fasta \
    --checkpoint=checkpoint-50 \
    --output=output.fastq \
    --batch_zmws=100