MaSuRCA

Description

masurca website

MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454).

Environment Modules

Run module spider masurca to find out what environment modules are available for this application.

Environment Variables

• HPC_MASURCA_DIR - installation directory
• HPC_MASURCA_BIN - executable directory
• HPC_MASURCA_NET - network file directory

Additional Usage Information

You can find the sample configuration file sr_config_example.txt is available in the $HPC_MASURCA_CFG directory.

A superreads.pl script distributed by the Stringtie project and modified for use on HiPerGator is available starting with masurca/3.2.1.

Citation

If you publish research that uses masurca you have to cite it as follows:

Zimin, A. et al. The MaSuRCA genome Assembler. Bioinformatics (2013). doi:10.1093/bioinformatics/btt476

Categories

biology, alignment