Difference between revisions of "LoRMA"
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[[Category:Software]][[Category:Biology]][[Category:NGS]] | [[Category:Software]][[Category:Biology]][[Category:NGS]] | ||
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
| − | |{{#vardefine:app| | + | |{{#vardefine:app|lorma}} |
| − | |{{#vardefine:url|https:// | + | |{{#vardefine:url|https://www.cs.helsinki.fi/u/lmsalmel/LoRMA/}} |
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:job|}} <!--JOB SCRIPTS--> | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
|{{#vardefine:faq|}} <!--FAQ--> | |{{#vardefine:faq|}} <!--FAQ--> | ||
| − | |{{#vardefine:citation|}} <!--CITATION--> | + | |{{#vardefine:citation|1}} <!--CITATION--> |
|{{#vardefine:installation|}} <!--INSTALLATION--> | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
|} | |} | ||
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
| − | LoRMA is a tool for correcting sequencing errors in long reads | + | LoRMA is a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines. |
<!--Modules--> | <!--Modules--> | ||
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | + | LoRMA needs to be launched for access to LoRMA and lordec binaries. Run the programs listed below with | |
| + | |||
| + | module load lorma | ||
| + | launch_lorma <executable> <arguments> | ||
| + | where executables include | ||
| + | :h5dump | ||
| + | :lordec-build-SR-graph | ||
| + | :lordec-correct | ||
| + | :lordec-stat | ||
| + | :lordec-trim | ||
| + | :lordec-trim-split | ||
| + | :LoRMA | ||
| + | :lorma.sh | ||
|}} | |}} | ||
| Line 58: | Line 70: | ||
If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} you have to cite it as follows: | ||
| − | + | L. Salmela, R. Walve, E. Rivals, and E. Ukkonen: Accurate selfcorrection of errors in long reads using de Bruijn graphs. Accepted to RECOMB-Seq 2016. | |
|}} | |}} | ||
Latest revision as of 14:34, 18 October 2022
Description
LoRMA is a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines.
Environment Modules
Run module spider lorma to find out what environment modules are available for this application.
System Variables
- HPC_LORMA_DIR - installation directory
Additional Information
LoRMA needs to be launched for access to LoRMA and lordec binaries. Run the programs listed below with
module load lorma launch_lorma <executable> <arguments>
where executables include
- h5dump
- lordec-build-SR-graph
- lordec-correct
- lordec-stat
- lordec-trim
- lordec-trim-split
- LoRMA
- lorma.sh
Citation
If you publish research that uses lorma you have to cite it as follows:
L. Salmela, R. Walve, E. Rivals, and E. Ukkonen: Accurate selfcorrection of errors in long reads using de Bruijn graphs. Accepted to RECOMB-Seq 2016.