Difference between revisions of "Reptile"
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*Makes simple use of quality score information. | *Makes simple use of quality score information. | ||
*Reptile has been developed by Xiao Yang, Karin Dorman and Srinivas Aluru. | *Reptile has been developed by Xiao Yang, Karin Dorman and Srinivas Aluru. | ||
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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}}. | ||
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{{App_Location|app={{#var:app}}|{{#var:ver}}}} | {{App_Location|app={{#var:app}}|{{#var:ver}}}} | ||
| − | + | ==Available Versions== | |
| + | * 1.1 | ||
| + | * 1.1 OMP (parallelized) | ||
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{{#if: {{#var: mod}}|==Running the application using modules== | {{#if: {{#var: mod}}|==Running the application using modules== | ||
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| + | * HPC_REPTILE_BIN - Executable directory | ||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
| − | + | 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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Revision as of 20:13, 18 June 2012
Description
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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:
- 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.