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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==Available Versions== | ==Available Versions== | ||
* 1.1 (serial, and parallelized OMP and Intel/OMP versions) | * 1.1 (serial, and parallelized OMP and Intel/OMP versions) | ||
Revision as of 02:00, 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.
Available Versions
- 1.1 (serial, and parallelized OMP and Intel/OMP versions)
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
- HPC_REPTILE_CONF - Sample configuration files
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.
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.