Difference between revisions of "Reptile"
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| − | [[Category:Software]] | + | [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Math]] |
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|{{#vardefine:app|reptile}} | |{{#vardefine:app|reptile}} | ||
|{{#vardefine:url|http://aluru-sun.ece.iastate.edu/doku.php?id=reptile}} | |{{#vardefine:url|http://aluru-sun.ece.iastate.edu/doku.php?id=reptile}} | ||
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|{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | |{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | ||
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
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|{{#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 --> |
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<!-- ######## Template Body ######## --> | <!-- ######## Template Body ######## --> | ||
<!--Description--> | <!--Description--> | ||
{{#if: {{#var: url}}| | {{#if: {{#var: url}}| | ||
| − | {{App_Description|app={{#var:app}}|url={{#var:url}}}}|}} | + | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} |
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Reptile is a software developed in C++ for correcting sequencing errors in short reads from next-gen sequencing platforms. Reptile has several favorable properties: | Reptile is a software developed in C++ for correcting sequencing errors in short reads from next-gen sequencing platforms. Reptile has several favorable properties: | ||
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[http://aluru-sun.ece.iastate.edu/doku.php?id=reptile Upstream documentation] for {{#var:app}}. | [http://aluru-sun.ece.iastate.edu/doku.php?id=reptile Upstream documentation] for {{#var:app}}. | ||
| − | <!-- | + | <!--Modules--> |
| − | + | ==Environment Modules== | |
| − | = | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. |
| − | + | ==System Variables== | |
| − | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | |
| − | < | ||
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| − | {{ | ||
* HPC_REPTILE_BIN - Executable directory | * HPC_REPTILE_BIN - Executable directory | ||
| − | {{#if: {{#var: exe}}|== | + | * HPC_REPTILE_CONF - Sample configuration files |
| + | <!--Additional--> | ||
| + | {{#if: {{#var: exe}}|==Additional Information== | ||
Make sure that the environmental variable <code>OMP_NUM_THREADS</code> is set to the number of threads you wish to use when executing Reptile when using the reptile-omp binary. | Make sure that the environmental variable <code>OMP_NUM_THREADS</code> is set to the number of threads you wish to use when executing Reptile when using the reptile-omp binary. | ||
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| + | There is a [http://aluru-sun.ece.iastate.edu/doku.php?id=reptile_tutorial reptile tutorial] written by Daniel S. Standage. | ||
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| + | The available binaries and scripts include: | ||
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| + | fastq-converter reptile_merger reptile-omp reptile-omp-intel reptile-v1.1 seq-analy. | ||
| + | |||
| + | Sample configuration files are in $HPC_REPTILE_CONF | ||
|}} | |}} | ||
{{#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 | + | {{#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. | |
|}} | |}} | ||
Latest revision as of 21:46, 21 August 2022
Description
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.
Environment Modules
Run module spider reptile to find out what environment modules are available for this application.
System Variables
- HPC_REPTILE_DIR - installation directory
- HPC_REPTILE_BIN - Executable directory
- HPC_REPTILE_CONF - Sample configuration files
Additional Information
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.
There is a reptile tutorial written by Daniel S. Standage.
The available binaries and scripts include:
fastq-converter reptile_merger reptile-omp reptile-omp-intel reptile-v1.1 seq-analy.
Sample configuration files are in $HPC_REPTILE_CONF
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.