Details

Autor(en) / Beteiligte

• Hu, Jiang
• Fan, Junpeng
• Sun, Zongyi
• Liu, Shanlin
• Berger, Bonnie

Titel

NextPolish: a fast and efficient genome polishing tool for long-read assembly

Ist Teil von

• Bioinformatics, 2020-04, Vol.36 (7), p.2253-2255

Ort / Verlag

England: Oxford University Press

Erscheinungsjahr

2020

Link zum Volltext

Quelle

Free E-Journal (出版社公開部分のみ）

Beschreibungen/Notizen

• Abstract Motivation Although long-read sequencing technologies can produce genomes with long contiguity, they suffer from high error rates. Thus, we developed NextPolish, a tool that efficiently corrects sequence errors in genomes assembled with long reads. This new tool consists of two interlinked modules that are designed to score and count K-mers from high quality short reads, and to polish genome assemblies containing large numbers of base errors. Results When evaluated for the speed and efficiency using human and a plant (Arabidopsis thaliana) genomes, NextPolish outperformed Pilon by correcting sequence errors faster, and with a higher correction accuracy. Availability and implementation NextPolish is implemented in C and Python. The source code is available from https://github.com/Nextomics/NextPolish. Supplementary information Supplementary data are available at Bioinformatics online.