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

Christina J. Castro; Rachel L. Marine; Edward Ramos; Terry Fei Fan Ng

The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/815480 doi: bioRxiv preprint Even with an adequate depth of coverage for genome reconstruction, assembly of total reads (T) in 187 11/12 experiments resulted in unresolved genome construction -resulting in numerous fragmented viral 188 contigs [ Figure 6 ]. The only exception was one experiment where one single PeV-A3 (S1) genome was 189 assembled using Cap3. When only reads from the major variant were assembled (M), full genomes were 190 obtained for all datasets using SPAdes and Cap3, and for the CV-B5 sample using Geneious. Conversely, 191 assembly of the read bins containing major and minor variants (Mm) resulted in an increased number of 192 contigs for 9 of the 12 sample and assembly software combinations tested [ Figure 6 ], indicating that VI due to Several experiments using simulated and clinical sample NGS data were performed to evaluate the 212 ability of genome assembly programs to distinguish genome variants. All assemblers investigated generated 213 fragmented assemblies when the data contained reads from two closely related variants due to "variant 214 interference" (VI). Changes in pairwise identity (PID) as small as 0.01% between the two variants triggered an 215 All rights reserved. No reuse allowed without permission.