Difference between revisions of "MaSuRCA"
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| − | < | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. |
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory | ||
| + | * HPC_{{uc:{{#var:app}}}}_CFG - sample configuration file directory | ||
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | + | You can find the sample configuration file sr_config_example.txt is available in the '<code>$HPC_MASURCA_CFG</code>' directory. | |
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| + | A superreads.pl script distributed by the [http://ccb.jhu.edu/software/stringtie/dl/ Stringtie] project and modified for use on HiPerGator is available starting with masurca/3.2.1. | ||
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Latest revision as of 18:24, 18 August 2022
Description
MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454).
Environment Modules
Run module spider masurca to find out what environment modules are available for this application.
System Variables
- HPC_MASURCA_DIR - installation directory
- HPC_MASURCA_BIN - executable directory
- HPC_MASURCA_CFG - sample configuration file directory
Additional Information
You can find the sample configuration file sr_config_example.txt is available in the '$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