RECKONER: Read Error Corrector Based on KMC
Overview
Authors
Affiliations
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 4 GB of RAM in about 35 min 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.
A survey of k-mer methods and applications in bioinformatics.
Moeckel C, Mareboina M, Konnaris M, Chan C, Mouratidis I, Montgomery A Comput Struct Biotechnol J. 2024; 23:2289-2303.
PMID: 38840832 PMC: 11152613. DOI: 10.1016/j.csbj.2024.05.025.
MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS reads.
Sami A, El-Metwally S, Rashad M BMC Bioinformatics. 2024; 25(1):61.
PMID: 38321434 PMC: 10848413. DOI: 10.1186/s12859-024-05681-1.
Illumina reads correction: evaluation and improvements.
Dlugosz M, Deorowicz S Sci Rep. 2024; 14(1):2232.
PMID: 38278837 PMC: 11222498. DOI: 10.1038/s41598-024-52386-9.
Wang Z, Fu L, Yu E, Zhu W, Zeng S, Cao H DNA Res. 2023; 31(1).
PMID: 38147541 PMC: 10781514. DOI: 10.1093/dnares/dsad028.
On Bridging Paired-end RNA-seq Data.
Li X, Shao M ACM BCB. 2023; 2023.
PMID: 38045531 PMC: 10692976. DOI: 10.1145/3584371.3612987.