deepconsensus
Link to section 'Introduction' of 'deepconsensus' Introduction
DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.
Docker hub: https://hub.docker.com/r/google/deepconsensus
Home page: https://github.com/google/deepconsensus
Link to section 'Versions' of 'deepconsensus' Versions
- 0.2.0
Link to section 'Commands' of 'deepconsensus' Commands
- deepconsensus
- ccs
- actc
Link to section 'Module' of 'deepconsensus' Module
You can load the modules by:
module load biocontainers
module load deepconsensus
Link to section 'Example job' of 'deepconsensus' 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 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