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Reptile | Representative tiling for short read error correction

Allows users to correct errors in short-read data from next-generation sequencing (NGS). Reptile is a scalable short-read error correction method broadly based on the k-mer spectrum approach, but that also uses adjoining k-mer information (called tiles) to reliably suggest error corrections. The software was evaluated on several Illumina/Solexa datasets. A distributed memory approach to parallelization of Reptile allows hardware (with any memory size per node) to be employed for error correction of any dataset using Reptile’s algorithm.

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Reptile forum

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Reptile classification

Reptile specifications

Unique identifier:
OMICS_01109
Interface:
Command line interface
Operating system:
Unix/Linux
License:
GNU General Public License version 3.0
Version:
1.1
Requirements:
Perl, GNU make, C++ compiler
Software type:
Package/Module
Restrictions to use:
None
Programming languages:
C++
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes

Reptile distribution

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Reptile support

Maintainers

  • Srinivas Aluru <>
  • Vipin Sachdeva <>
  • David Bader <>

Credits

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Publications

Institution(s)

Computational Science Center IBM T. J. Watson Research, Cambridge, MA, USA; Georgia Institute of Technology, Atlanta, GA, USA; Georgia Institute of Technology, Atlanta, GA, USA

Funding source(s)

A parallelized version is available at http://aluru-sun.ece.iastate.edu/lib/exe/fetch.php?media=source:reptile-omp.tar.bz2
Tutorial: http://aluru-sun.ece.iastate.edu/doku.php?id=reptile_tutorial

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