GMcloser: Difference between revisions
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Created page with "Category:SoftwareCategory:BiologyCategory:NGS {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|gmcloser}} |{{#vardefine:url|https://sourceforge.net/projects/gmcl..." |
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==System Variables== | ==System Variables== | ||
* HPC_{{ | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
* HPC_{{ | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory | ||
<!--Configuration--> | <!--Configuration--> | ||
Revision as of 21:20, 6 December 2019
Description
GMcloser fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads. Unlike other gap-closing tools that use only NGS reads, GMcloser uses preassembled contig sets or long read sets as the sequences to close gaps and uses paired-end (PE) reads and a likelihood-based algorithm to improve the accuracy and efficiency of gap closure. The efficiency of gap closure can be increased by successive treatments with different contig sets.
Required Modules
Serial
- gmcloser
System Variables
- HPC_GMCLOSER_DIR - installation directory
- HPC_GMCLOSER_BIN - executable directory