MaSuRCA: Difference between revisions
Moskalenko (talk | contribs) Created page with "Category:SoftwareCategory:BioinformaticsCategory:NGS {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|masurca}} |{{#vardefine:url|http://www.genome.umd.edu/masur..." |
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|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
|{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> | ||
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
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== | ==Environment Modules== | ||
< | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==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 | |||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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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>$HPC_MASURCA_CFG</code>' directory. | |||
A superreads.pl script distributed by the [http://ccb.jhu.edu/software/stringtie/dl/ Stringtie] project and modified for use on HiPerGator is available starting with masurca/3.2.1. | |||
|}} | |}} | ||
Latest revision as of 18:24, 18 August 2022
Description
MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454).
Environment Modules
Run module spider masurca to find out what environment modules are available for this application.
System Variables
- HPC_MASURCA_DIR - installation directory
- HPC_MASURCA_BIN - executable directory
- HPC_MASURCA_CFG - sample configuration file directory
Additional Information
You can find the sample configuration file sr_config_example.txt is available in the '$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