wtdbg2
wtdbg2 is a fast de novo assembly tool for long-read sequence data produced by PacBio or Oxford Nanopore Technologies sequencers.
License
Free to use and open source under GNU GPLv3.
Available
- Roihu-CPU: 2.5, via the
bio-appsmodule.
Usage
wtdbg2 is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the wtdbg2 module:
After that, you can use the wtdbg2 assembler and the wtpoa-cns consenser. wtdbg2 assembles raw reads and generates the contig layout and edge sequences in a file prefix.ctg.lay.gz. Executable wtpoa-cns takes this file as input and produces the final consensus in FASTA.
A typical workflow looks like this:
wtdbg2 -x rs -g 4.6m -t 16 -i reads.fa.gz -fo prefix
wtpoa-cns -t 16 -i prefix.ctg.lay.gz -fo prefix.ctg.fa
In the wtdbg2 command, -g is the estimated genome size and -x specifies the sequencing technology, which could take value rs for PacBio RSII, sq for PacBio Sequel, ccs for PacBio CCS reads and ont for Oxford Nanopore. This option sets multiple parameters and should be applied before other parameters. When you are unable to get a good assembly, you may need to tune other parameters as described in the wtdbg2 manual.
In the case of any large (more than 10 Mb) genomes, wtdbg2 assembly process can take several hours or days. On Roihu, such large tasks should always be executed as batch jobs.
Below is a sample batch job file for assembling C. elegans genome.
The sample dataset (about 16 GB) was downloaded from the ENA database with the command:
The actual assembly task was executed with the batch job below:
#!/bin/bash
#SBATCH --job-name=wtdbg2
#SBATCH --account=<project>
#SBATCH --time=12:00:00
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --cpus-per-task=32
#SBATCH --mem=64G
#SBATCH --partition=small
module load bio-apps/v202603
module load wtdbg2/2.5
wtdbg2 -x rs -g100m -t $SLURM_CPUS_PER_TASK -i SRR5439404_subreads.fastq.gz -fo c_elegans_test
wtpoa-cns -t $SLURM_CPUS_PER_TASK -i c_elegans_test.ctg.lay.gz -fo c_elegans.ctg.fa
In the example above <project> should be replaced with your project name. You can use csc-projects to check your CSC projects. Maximum running time is set to 12 hours (--time=12:00:00). As wtdbg2 uses thread-based parallelization, the process is considered as one job that should be executed within one node (--nodes=1, --ntasks=1). The job reserves 32 cores --cpus-per-task=32 that can use in total up to 64 GB of memory (--mem=64G). Note that the number of cores to be used needs to be defined in wtdbg2 and wtpoa-cns commands too. This can be set with the option -t. In this case, we use $SLURM_CPUS_PER_TASK variable that contains the --cpus-per-task value (we could as well use -t 32, but then we have to remember to change the value if the number of the reserved CPUs is changed later).
The job is submitted to the batch job system with sbatch command. For example, if the batch job
file is named wtdbg2_job.sh, then the submission command is:
See creating a batch job script for Roihu for more information about running batch jobs.