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 default 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