Difference between revisions of "Reptile"
Moskalenko (talk | contribs) |
Moskalenko (talk | contribs) |
||
| Line 26: | Line 26: | ||
|{{#vardefine:testing|}} <!--Enable performance testing/profiling section --> | |{{#vardefine:testing|}} <!--Enable performance testing/profiling section --> | ||
|{{#vardefine:faq|}} <!--Enable FAQ section --> | |{{#vardefine:faq|}} <!--Enable FAQ section --> | ||
| − | |{{#vardefine:citation|}} <!--Enable Reference/Citation section --> | + | |{{#vardefine:citation|1}} <!--Enable Reference/Citation section --> |
|} | |} | ||
<!-- ######## Template Body ######## --> | <!-- ######## Template Body ######## --> | ||
| Line 46: | Line 46: | ||
* 1.1 | * 1.1 | ||
* 1.1 OMP (parallelized) | * 1.1 OMP (parallelized) | ||
| − | |||
{{#if: {{#var: mod}}|==Running the application using modules== | {{#if: {{#var: mod}}|==Running the application using modules== | ||
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | ||
| Line 54: | Line 53: | ||
|}} | |}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
| − | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | + | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details. |
| + | |}} | ||
{{#if: {{#var: pbs}}|==PBS Script Examples== | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
{{#if: {{#var: policy}}|==Usage policy== | {{#if: {{#var: policy}}|==Usage policy== | ||
| − | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | + | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used) |
| + | |}} | ||
{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
WRITE PERFORMANCE TESTING RESULTS HERE|}} | WRITE PERFORMANCE TESTING RESULTS HERE|}} | ||
{{#if: {{#var: faq}}|==FAQ== | {{#if: {{#var: faq}}|==FAQ== | ||
| − | *'''Q:''' **'''A:'''|}} | + | *'''Q:''' **'''A:''' |
| + | |}} | ||
{{#if: {{#var: citation}}|==Citation== | {{#if: {{#var: citation}}|==Citation== | ||
| − | If you publish research that uses {{ | + | If you publish research that uses {{#var: app}} you have to cite it as follows: |
| − | + | X. Yang, K. Dorman and S. Aluru, “Reptile: Representative tiling for short read error correction”, Bioinformatics, 26(20), 2526-2533, 2010. | |
|}} | |}} | ||
Revision as of 20:17, 18 June 2012
Description
{{{name}}} website
Reptile is a software developed in C++ for correcting sequencing errors in short reads from next-gen sequencing platforms. Reptile has several favorable properties:
- Memory efficiency. Reptile can process input data with sizes larger than main memory. For instance, to process a 160x coverage (3.8GB) Illumina data for E. coli it requires only ~1GB memory, which is easily available in a desktop computer.
- High speed. Processing Illumina data for a microbe typically takes 0.5hr ~ 2hrs, depending on the number and the quality of reads.
- Can handle reads containing non-acgt characters and reads with non-equal length.
- Makes simple use of quality score information.
- Reptile has been developed by Xiao Yang, Karin Dorman and Srinivas Aluru.
Upstream documentation for reptile. Template:App Location
Available Versions
- 1.1
- 1.1 OMP (parallelized)
Running the application using modules
To use reptile with the environment modules system at HPC the following commands are available:
Get module information for reptile:
$module spider reptile
Load the default application module:
$module load reptile
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_REPTILE_DIR - directory where reptile is located.
- HPC_REPTILE_BIN - Executable directory
How To Run
Make sure that the environmental variable OMP_NUM_THREADS is set to the number of threads you wish to use when executing Reptile when using the reptile-omp binary.
Citation
If you publish research that uses reptile you have to cite it as follows: X. Yang, K. Dorman and S. Aluru, “Reptile: Representative tiling for short read error correction”, Bioinformatics, 26(20), 2526-2533, 2010.