Masurca

Description

The MaSuRCA (Maryland Super Read Cabog Assembler) genome assembly and analysis toolkit contains of MaSuRCA genome assembler, QuORUM error corrector for Illumina data, POLCA genome polishing software, Chromosome scaffolder, jellyfish mer counter, and MUMmer aligner. The usage instructions for the additional tools that are exclusive to MaSuRCA, such as POLCA and Chromosome scaffolder are provided at the end of this Guide. The MaSuRCA assembler combines the benefits of deBruijn graph and Overlap-Layout-Consensus assembly approaches. Since version 3.2.1 it supports hybrid assembly with short Illumina reads and long high error PacBio/MinION data.

License

GNU General Public License v3.0

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of masurca and load default version of masurca as

module avail masurca/ # list available modules
module load masurca   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail masurca

and choose explicit version you want to use.

Masurca launches helper processes that use additional CPUs. So the total CPU usage is higher than is defined by the NUM_THREADS parameter in the configuration file. Therefore, to prevent the termination of calculation by the scheduling system due to exceeding the number of reserved CPUs, reserve 3 extra CPUs.

-l select=1:ncpus=X+3
NUM_THREADS=X

Documentation

https://github.com/alekseyzimin/masurca#3-running-the-masurca-assembler

Homepage

http://genome.umd.edu/masurca.html and https://github.com/alekseyzimin/masurca#masurca-genome-assembly-and-analysis-toolkit-quick-start-guide