Apclusterv: Refinement of Viral Genome Clustering with Affinity Propagation DOI Creative Commons

Yao Haobin,

Ruishi Liang,

Xiong Zhongyu

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 28, 2024

Abstract Background Clustering assemblies is a fundamental process of metagenomic analysis. In an era where researchers from variety export domains are conducting heavy efforts on viral metagenomics, unsupervised clustering becomes critical bioinformatics tool to overcome the shortage reference genomes with known taxonomy information. Results Here we present Apclusterv, novel software for genome in manner. Our pipeline relies gene prediction contigs and protein sequence alignment. The program implemented as open-source Python package. Apclusterv integrates two procedures: Markov (MCL) Affinity Propagation (AP). MCL AP both algorithms that can determine number clusters automatically. Also, they display great synergy our work. task genomes, algorithm shows significant improvement quality obtained. freely available at https://github.com/hbyaoherbert/Apclusterv Conclusions Assemblies reads largely incomplete. resolves limitation short-reads assembly by identifying confident local alignments through self-adaptive system. give accurate genera-level contigs, which subsequent classification, Operation Taxonomy Unit (OUT) construction, or gene-sharing network

Language: Английский

Apclusterv: Refinement of Viral Genome Clustering with Affinity Propagation DOI Creative Commons

Yao Haobin,

Ruishi Liang,

Xiong Zhongyu

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 28, 2024

Abstract Background Clustering assemblies is a fundamental process of metagenomic analysis. In an era where researchers from variety export domains are conducting heavy efforts on viral metagenomics, unsupervised clustering becomes critical bioinformatics tool to overcome the shortage reference genomes with known taxonomy information. Results Here we present Apclusterv, novel software for genome in manner. Our pipeline relies gene prediction contigs and protein sequence alignment. The program implemented as open-source Python package. Apclusterv integrates two procedures: Markov (MCL) Affinity Propagation (AP). MCL AP both algorithms that can determine number clusters automatically. Also, they display great synergy our work. task genomes, algorithm shows significant improvement quality obtained. freely available at https://github.com/hbyaoherbert/Apclusterv Conclusions Assemblies reads largely incomplete. resolves limitation short-reads assembly by identifying confident local alignments through self-adaptive system. give accurate genera-level contigs, which subsequent classification, Operation Taxonomy Unit (OUT) construction, or gene-sharing network

Language: Английский

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