AliMarko: A Pipeline for Virus Identification Using an Expert-Guided Approach

Area of Science:

• Virology
• Bioinformatics
• Metagenomics

Background:

• Viruses are widespread and pose health risks, but their genetic diversity complicates analysis.
• Identifying viruses in metagenomic samples is challenging due to the absence of universal marker genes.

Purpose of the Study:

• To develop a robust pipeline for comprehensive virus identification in metagenomic data.
• To improve the detection of diverse and low-coverage viral sequences.

Main Methods:

• Developed the AliMarko pipeline, employing a dual approach: reference-based read mapping and de novo assembly with HMM-based homology search.
• Integrated phylogenetic analysis for sequence validation and relationship assessment.
• Applied the pipeline to total RNA sequencing data from bat feces.

Main Results:

• Successfully identified a range of viruses in bat fecal samples.
• Demonstrated the pipeline's capability to detect low-coverage and divergent viral sequences.
• Enabled rapid validation and phylogenetic assessment of identified viral sequences.

Conclusions:

• The AliMarko pipeline offers a comprehensive solution for virus identification in metagenomic studies.
• This tool facilitates the interpretation of viral communities and advances understanding of viral diversity.
• AliMarko is a valuable resource for researchers studying viruses and their impact on health.