Difference between revisions of "Reptile"
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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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==Required Modules== | ==Required Modules== | ||
[[Modules|modules documentation]] | [[Modules|modules documentation]] | ||
| − | ===Serial=== | + | ===Serial and Parallel (OMP)=== |
*{{#var:app}} | *{{#var:app}} | ||
| + | ===Parallel (OpenMP)=== | ||
| + | ==System Variables== | ||
| + | * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | ||
* HPC_REPTILE_BIN - Executable directory | * HPC_REPTILE_BIN - Executable directory | ||
* HPC_REPTILE_CONF - Sample configuration files | * HPC_REPTILE_CONF - Sample configuration files | ||
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| + | {{#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. | ||
Revision as of 19:39, 10 August 2012
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.
Required Modules
Serial and Parallel (OMP)
- reptile
Parallel (OpenMP)
System Variables
- HPC_{{#uppercase: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.