HMMPolish: a coding region polishing tool for TGS-sequenced RNA viruses.

ABSTRACT: Access to accurate viral genomes is important to downstream data analysis. Third-generation sequencing (TGS) has recently become a popular platform for virus sequencing because of its long read length. However, its per-base error rate, which is higher than next-generation sequencing, can lead to genomes with errors. Polishing tools are thus needed to correct errors either before or after sequence assembly. Despite promising results of available polishing tools, there is still room to improve the error correction performance to perform more accurate genome assembly. The errors, particularly those in coding regions, can hamper analysis such as linage identification and variant monitoring. In this work, we developed a novel pipeline, HMMPolish, for correcting (polishing) errors in protein-cod

SUBMITTER: Yu R 

PROVIDER: S-EPMC10516367 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature