Literature DB >> 28062451

RECKONER: read error corrector based on KMC.

Maciej Dlugosz, Sebastian Deorowicz.   

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 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.
© The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

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Mesh：

Year:  2017        PMID： 28062451     DOI： 10.1093/bioinformatics/btw746

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  5 in total

Review 1.  Genome sequence assembly algorithms and misassembly identification methods.

Authors:  Yue Meng; Yu Lei; Jianlong Gao; Yuxuan Liu; Enze Ma; Yunhong Ding; Yixin Bian; Hongquan Zu; Yucui Dong; Xiao Zhu
Journal:  Mol Biol Rep       Date:  2022-09-23       Impact factor: 2.742

2.  CARE 2.0: reducing false-positive sequencing error corrections using machine learning.

Authors:  Felix Kallenborn; Julian Cascitti; Bertil Schmidt
Journal:  BMC Bioinformatics       Date:  2022-06-13       Impact factor: 3.307

3.  The genome of the Paleogene relic tree Bretschneidera sinensis: insights into trade-offs in gene family evolution, demographic history, and adaptive SNPs.

Authors:  Hai-Lin Liu; A J Harris; Zheng-Feng Wang; Hong-Feng Chen; Zhi-An Li; Xiao Wei
Journal:  DNA Res       Date:  2022-01-28       Impact factor: 4.477

4.  Benchmarking of computational error-correction methods for next-generation sequencing data.

Authors:  Keith Mitchell; Jaqueline J Brito; Igor Mandric; Qiaozhen Wu; Sergey Knyazev; Sei Chang; Lana S Martin; Aaron Karlsberg; Ekaterina Gerasimov; Russell Littman; Brian L Hill; Nicholas C Wu; Harry Taegyun Yang; Kevin Hsieh; Linus Chen; Eli Littman; Taylor Shabani; German Enik; Douglas Yao; Ren Sun; Jan Schroeder; Eleazar Eskin; Alex Zelikovsky; Pavel Skums; Mihai Pop; Serghei Mangul
Journal:  Genome Biol       Date:  2020-03-17       Impact factor: 13.583

5.  Polyphenism of a Novel Trait Integrated Rapidly Evolving Genes into Ancestrally Plastic Networks.

Authors:  Sofia Casasa; Joseph F Biddle; Georgios D Koutsovoulos; Erik J Ragsdale
Journal:  Mol Biol Evol       Date:  2021-01-23       Impact factor: 16.240
  5 in total

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