Difference between revisions of "MaSuRCA"

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==Required Modules==
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==Environment Modules==
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==System Variables==
 
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You can find the sample configuration file sr_config_example.txt is available in the '<code>$HPC_MASURCA_CFG</code>' directory.
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A superreads.pl script distributed by the [http://ccb.jhu.edu/software/stringtie/dl/ Stringtie] project and modified for use on HiPerGator is available starting with masurca/3.2.1.
  
 
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Revision as of 17:47, 10 June 2022

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.

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.



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