Virseqimprover: an integrated pipeline for viral contig error correction, extension, and annotation.

ABSTRACT: Despite the recent surge of viral metagenomic studies, it remains a significant challenge to recover complete virus genomes from metagenomic data. The majority of viral contigs generated from de novo assembly programs are highly fragmented, presenting significant challenges to downstream analysis and inference. To address this issue, we have developed Virseqimprover, a computational pipeline that can extend assembled contigs to complete or nearly complete genomes while maintaining extension quality. Virseqimprover first examines whether there is any chimeric sequence based on read coverage, breaks the sequence into segments if there is, then extends the longest segment with uniform depth of coverage, and repeats these procedures until the sequence cannot be extended. Finally, Virseqimprove

SUBMITTER: Song H 

PROVIDER: S-EPMC11727651 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature