Fec

'Fec' is a fast and efficient error correction tool designed for third-generation sequencing data, which often contains long reads with relatively high error rates. Error correction is a critical preprocessing step in the analysis of these long-read sequences. 'Fec' specifically addresses the challenges associated with error correction in high-coverage scenarios, where the process can be time-consuming.
The tool leverages overlapping reads to identify and correct errors. 'Fec' operates in two rounds, utilizing a combination of large and small window sizes. In the first round, a relatively large window size is used to quickly identify sufficient overlaps between reads, enabling the correction of most reads. In the second round, a smaller window size is employed to identify additional overlaps, focusing on reads that may not have been adequately corrected in the first round.
'Fec' uses caching for base-level alignment information. When performing alignment, 'Fec' first checks a cache for existing alignments. If the alignment is found in the cache, 'Fec' retrieves it and deduces the second alignment from it. This caching strategy significantly reduces the need for repeated alignment calculations, making the error correction process more efficient.
The Authors have tested the tool on nine datasets, including both PacBio and nanopore sequencing data, and the results demonstrate that 'Fec' offers a substantial speed improvement compared to other error correction methods like MECAT, CANU, MINICNS, and NECAT, especially in scenarios with high-coverage data.
'Fec' is available for use either as a standalone tool or as part of an assembly pipeline.