Difference between revisions of "MaSuRCA"

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==System Variables==
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{#uppercase:{{#var:app}}}}_BIN - executable directory
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
* HPC_{{#uppercase:{{#var:app}}}}_CFG - sample configuration file directory
* HPC_{{uc:{{#var:app}}}}_CFG - sample configuration file directory
{{#if: {{#var: conf}}|==Configuration==
{{#if: {{#var: conf}}|==Configuration==

Revision as of 21:21, 6 December 2019


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).

Required Modules

System Variables

  • HPC_MASURCA_DIR - installation directory
  • HPC_MASURCA_BIN - executable directory
  • HPC_MASURCA_CFG - sample configuration file directory

Additional 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.


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