Third generation DNA sequencing technologies yield long, but error rich sequencing reads, while second generation technologies yield short read with low error rate. Hence, the need for correcting the long reads.
LoRDEC is a program for error correcting long sequencing reads using short reads. It implements a hybrid correction approach. It uses little memory and is very efficient. Most importantly it scales up to process very large data sets. It can be applied to long reads obtained with either Pacific Biosciences SMRT sequencing (SMRT = Single Molecule Real Time) or with Oxford Nanopore MINion technology.
L. Salmela, E. Rivals. (2014) LoRDEC: accurate and efficient long read error correction
Bioinformatics, 30 (24): 3506-3514, 2014.
LoRDEC is available as a binary for immediate use on Linux platform, with the following requirements:
|Linux running on Intel or AMD 64bit processors.
(kernel 2.6.32 or above, GLIBCXX_3.4.13 or above)
For all other platforms or configurations, or if above binaries fail to run on your computer, you should download source code and compile it.
|LoRDEC tool is fully written in C++.||Download|
Documentation and specific support
Available here. LoRDEC specific support is available from Lirmm research team at firstname.lastname@example.org.
LoRDEC binaries and source code are covered by the CeCILL A license and GATB-CORE library by the Affero GPL version 3 license.