reptile

Description

reptile website

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. 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.

Environment Modules

Run module spider reptile to find out what environment modules are available for this application.

Environment Variables

• HPC_REPTILE_DIR - installation directory
• HPC_REPTILE_BIN - executable directory
• HPC_REPTILE_CONF - sample configuration files directory

Categories

biology, ngs, math