Difference between revisions of "YAHA"
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YAHA is a flexible, sensitive and accurate hash-based DNA aligner for relatively long queries that operates in three distinct modes. It can output all the alignments found for each query, only the set of alignments that optimally cover each query, or add alignments that are similar to those that optimally cover the query. These latter two modes are especially useful for finding split-read mappings used to accurately identify structural variation events. | YAHA is a flexible, sensitive and accurate hash-based DNA aligner for relatively long queries that operates in three distinct modes. It can output all the alignments found for each query, only the set of alignments that optimally cover each query, or add alignments that are similar to those that optimally cover the query. These latter two modes are especially useful for finding split-read mappings used to accurately identify structural variation events. | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | < | + | 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 |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Latest revision as of 20:56, 12 August 2022
Description
YAHA is a flexible, sensitive and accurate hash-based DNA aligner for relatively long queries that operates in three distinct modes. It can output all the alignments found for each query, only the set of alignments that optimally cover each query, or add alignments that are similar to those that optimally cover the query. These latter two modes are especially useful for finding split-read mappings used to accurately identify structural variation events.
Environment Modules
Run module spider yaha to find out what environment modules are available for this application.
System Variables
- HPC_YAHA_DIR - installation directory
Citation
If you publish research that uses yaha you have to cite it as follows:
Citation: Faust GG and Hall IM. YAHA: fast and flexible long-read alignment with optimal breakpoint detection. Bioinformatics (2012) 28(19): 2417-2424. Epub 2012 Jul 24. doi:10.1093/bioinformatics.