Phables: from fragmented assemblies to high-quality bacteriophage genomes
01:46 Share

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.04.04.535632v1?rss=1

Authors: Mallawaarachchi, V., Roach, M. J., Papudeshi, B., Giles, S. K., Grigson, S. R., Decewicz, P., Bouras, G., Hesse, R. D., Inglis, L. K., Hutton, A. L., Dinsdale, E. A., Edwards, R. A.

Abstract: Microbial communities found within the human gut have a strong influence on human health. Intestinal bacteria and viruses influence gastrointestinal diseases such as inflammatory bowel disease. Viruses infecting bacteria, known as bacteriophages, play a key role in modulating bacterial communities within the human gut. However, the identification and characterisation of novel bacteriophages remain a challenge. Available tools use similarities between sequences, nucleotide composition, and the presence of viral genes/proteins. Most available tools consider individual contigs to determine whether they are of viral origin. As a result of the challenges in viral assembly, fragmentation of viral genomes can occur, leading to the need for new approaches in viral identification. We introduce Phables, a new computational method to resolve bacteriophage genomes from fragmented viral metagenomic assemblies. Phables identifies bacteriophage-like components in the assembly graph, models each component as a flow network, and uses graph algorithms and flow decomposition techniques to identify genomic paths. Experimental results of viral metagenomic samples obtained from different environments show that over 80% of the bacteriophage genomes resolved by Phables have high quality and are longer than the individual contigs identified by existing viral identification tools.

Copy rights belong to original authors. Visit the link for more info

Podcast created by Paper Player, LLC