Paper Info
Title
Fec: a fast error correction method based on two-rounds overlapping and caching
Abstract
The third-generation sequencing technology has advanced genome analysis with long-read length, but the reads need error correction due to the high error rate. Error correction is a time-consuming process especially when the sequencing coverage is high. Generally, for a pair of overlapping reads A and B, the existing error correction methods perform a base-level alignment from B to A when correcting the read A. And another base-level alignment from A to B is performed when correcting the read B. However, based on our observation, the base-level alignment information can be reused. In this article, we present a fast error correction tool Fec, using two-rounds overlapping and caching. Fec can be used independently or as an error correction step in an assembly pipeline. In the first round, Fec uses a large window size (20) to quickly find enough overlaps to correct most of the reads. In the second round, a small window size (5) is used to find more overlaps for the reads with insufficient overlaps in the first round. When performing base-level alignment, Fec searches the cache first. If the alignment exists in the cache, Fec takes this alignment out and deduces the second alignment from it. Otherwise, Fec performs base-level alignment and stores the alignment in the cache. We test Fec on nine datasets, and the results show that Fec has 1.24-38.56 times speed-up compared to MECAT, CANU and MINICNS on five PacBio datasets and 1.16-27.8 times speed-up compared to NECAT and CANU on four nanopore datasets.
Year
DOI
Venue
2022
10.1093/bioinformatics/btac565
BIOINFORMATICS
DocType
Volume
Issue
Journal
38
19
ISSN
Citations 
PageRank 
1367-4803
0
0.34
References 
Authors
0
6
Name
Order
Citations
PageRank
Jun Zhang103.04
Fan Nie200.34
Neng Huang322.40
Peng Ni463.80
Feng Luo528426.03
Jianxin Wang62163283.94