REFRESH Bioinformatics Group

RECKONER

RECKONER—What is it?

RECKONER (Read Error Corrector Based on KMC) is a tool for correction of genome sequencing reads. It is designed to correction of substitution errors, present especially in Illumina reads. Its idea is based on another algorithm—BLESS.

The architecture of RECKONER

RECKONER is implemented in C++ and uses bash script for call of its components—KMC and kmc_tools.

Terms of use of RECKONER

RECKONER is in general a free compression program available in both binary and source code releases. More details can be found out on download page.

Publications

+ Maciej Długosz, M., Deorowicz, S., RECKONER: read error corrector based on KMC, Bioinformatics, 2017; 33(7):1086–1089, Abstract.

Summary: Presence of sequencing errors in data produced by next-generation sequencers affects quality of downstream analyzes. Accuracy of them can be improved by performing error correction of sequencing reads. We introduce a new correction algorithm capable of processing eukaryotic close to 500 Mbp-genome-size, high error-rated data using less than 4GB of RAM in about 35min on 16-core computer.
Availability and Implementation: Program is freely available at http://sun.aei.polsl.pl/REFRESH/reckoner.
Contact: sebastian.deorowicz@polsl.pl
Supplementary information: Supplementary data are available at Bioinformatics online.