Benchmarking different approaches for Norovirus genome assembly in metagenome samples

• Published in: BMC genomics Vol. 22; no. 1; pp. 1 - 849
• Main Authors: Fuentes-Trillo, Azahara, Monzó, Carolina, Manzano, Iris, Santiso-Bellón, Cristina, Andrade, Juliana da Silva Ribeiro de, Gozalbo-Rovira, Roberto, García-García, Ana-Bárbara, Rodríguez-Díaz, Jesús, Chaves, Felipe Javier
• Format: Journal Article
• Language: English
• Published: London BioMed Central Ltd 24.11.2021; BioMed Central; BMC
• Subjects: Analysis; Assembly; Benchmarks; Bioinformatics; Care and treatment; Coexistence; Control; Diagnosis; Drug resistance; Gastroenteritis; Gene sequencing; Genome de-novo assembly; Genomes; Genomics; Graph theory; Identification and classification; Immune response; Metagenomics; Methodology; Methods; Mutation; Mutation rates; Norovirus; Prevention; Proteins; Risk factors; RNA polymerase; RNA viruses; Viruses; Workflow; Spain
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-021-08067-2

Genome assembly of viruses with high mutation rates, such as Norovirus and other RNA viruses, or from metagenome samples, poses a challenge for the scientific community due to the coexistence of several viral quasispecies and strains. Furthermore, there is no standard method for obtaining whole-genome sequences in non-related patients. After polyA RNA isolation and sequencing in eight patients with acute gastroenteritis, we evaluated two de Bruijn graph assemblers (SPAdes and MEGAHIT), combined with four different and common pre-assembly strategies, and compared those yielding whole genome Norovirus contigs. Reference-genome guided strategies with both host and target virus did not present any advantages compared to the assembly of non-filtered data in the case of SPAdes, and in the case of MEGAHIT, only host genome filtering presented improvements. MEGAHIT performed better than SPAdes in most samples, reaching complete genome sequences in most of them for all the strategies employed. Read binning with CD-HIT improved assembly when paired with different analysis strategies, and more notably in the case of SPAdes. Not all metagenome assemblies are equal and the choice in the workflow depends on the species studied and the prior steps to analysis. We may need different approaches even for samples treated equally due to the presence of high intra host variability. We tested and compared different workflows for the accurate assembly of Norovirus genomes and established their assembly capacities for this purpose.