Reptile
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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
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.