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

Area of Science:

• Bioinformatics
• Genomics
• Virology

Background:

• Viral metagenomic studies are increasing, but assembling complete viral genomes remains difficult.
• De novo assembly often yields fragmented viral contigs, hindering downstream analysis.

Purpose of the Study:

• To develop a computational pipeline, Virseqimprover, for extending fragmented viral contigs to complete or near-complete genomes.
• To improve the accuracy and completeness of viral genome assembly from metagenomic data.

Main Methods:

• Virseqimprover identifies and corrects chimeric sequences based on read coverage.
• It extends the longest sequence segments with uniform coverage until no further extension is possible.
• The pipeline annotates gene content of the resulting extended sequences.

Main Results:

• Virseqimprover effectively corrects and extends fragmented viral contigs to their complete lengths.
• The tool demonstrates good performance in improving viral contig completeness and minimizing assembly errors.
• Successful application leads to more complete viral genome reconstructions.

Conclusions:

• Virseqimprover is a valuable computational tool for enhancing viral genome assembly from metagenomic data.
• It addresses the challenge of fragmented contigs, providing researchers with more complete viral genomes.
• The pipeline is freely available as a web server and conda package.