MaSuRCA¶
MaSuRCA is an assembly algorithm for both PacBio and Illumina data that combines the benefits of De Bruijn graph and Overlap-Layout-Consensus assembly approaches.
MaSuRCA is available as a module on Apocrita.
Usage¶
To run the latest installed version of MaSuRCA, simply load the masurca
module:
$ module load masurca $ masurca USAGE: masurca <config_file>
For usage documentation, run masurca --help
.
Example job¶
Selecting the number of threads
To prevent overloading a compute node, you should include the
NUM_THREADS=X
parameter in your config file, where X
is equal to the
number of cores requested.
Serial Job¶
Here is an example job running on 2 cores and 4GB of memory:
#!/bin/bash #$ -cwd #$ -j y #$ -pe smp 2 #$ -l h_rt=1:0:0 #$ -l h_vmem=2G module load masurca masurca example.cfg ./assemble.sh
Here is the supporting example.cfg
file:
DATA PE= pe 180 20 /path/to/example.fastq END PARAMETERS GRAPH_KMER_SIZE=auto NUM_THREADS=2 JF_SIZE=200000000 END