The effect of variant interference on de novo assembly for viral deep sequencing.

ABSTRACT:

Background

Viruses have high mutation rates and generally exist as a mixture of variants in biological samples. Next-generation sequencing (NGS) approaches have surpassed Sanger for generating long viral sequences, yet how variants affect NGS de novo assembly remains largely unexplored.

Results

Our results from > 15,000 simulated experiments showed that presence of variants can turn an assembly of one genome into tens to thousands of contigs. This "variant interference" (VI) is highly consistent and reproducible by ten commonly-used de novo assemblers, and occurs over a range of genome length, read length, and GC content. The main driver of VI is pairwise identities between viral variants. These findings were further supported by in silico simulations, where selective remova

SUBMITTER: Castro CJ 

PROVIDER: S-EPMC7306937 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature