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Wtdbg2

Wtdbg2 is a de-novo sequence assembler for long noisy reads. It assembles raw reads without error correction and then builds the consensus from intermediate assembly output.

Wtdbg2 is available as a module on Apocrita.

Usage

To run the latest installed version of Wtdbg2, simply load the wtdbg2 module:

$ module load wtdbg2
$ wtdbg2 --help
Usage: wtdbg2 [options] -i <reads.fa> -o <prefix> [reads.fa ...]
...

For usage documentation, run wtdbg2 -h.

Core Usage

To ensure that Wtdbg2 always uses the correct number of cores, the -t ${NSLOTS} option should be used.

Example job

Serial job

Here is an example job running on 4 cores and 16GB total memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 4
#$ -l h_rt=24:0:0
#$ -l h_vmem=4G

module load wtdbg2

# Overlap and layout the reads
wtdbg2 -i assembly.ctg.lay.gz \
       -g 300M \
       -o outdir \
       -t ${NSLOTS}

# Derive consensus sequence for the contigs
wtpoa-cns -i assembly.ctg.lay.gz \
          -o outdir \
          -t ${NSLOTS}

Reference