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 default 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 ${NSLOTS} option should
be used.
Example job¶
Serial job¶
Here is an example job running on 4 cores and 16GB of memory:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 4
#$ -l h_rt=1:0:0
#$ -l h_vmem=4G
module load wtdbg2
# Overlap and layout the reads
wtdbg2 -i assembly.fa.gz \
-g 300M \
-o outdir \
-t ${NSLOTS}
# Derive consensus sequence for the contigs
wtpoa-cns -i assembly.ctg.lay.gz \
-o outdir \
-t ${NSLOTS}