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

De novo assembly programs (ABySS, BWA, Canu, Cap3, IDBA, MIRA, Newbler, SOAPdenovo, SPAdes, 91 Trinity, and Velvet) have increased from less than 1% of viral sequence entries in 2012, to 20% of all viral 92 sequence entries in 2017 [ Figure 1h & i]. A similar increase was observed for reference-mapping programs 93 (i.e., Bowtie and Bowtie2), from 0.03% in 2012 to 6.5% in 2017. Multifunctional programs (Suppl. Information) 94 that offer both assembly options were the most common programs cited for the years 2013-2017, but since 95 the exact sequence assembly strategy used for these records is unknown, the contributions of de novo 96 assembly are likely underestimated. An expanded summary of the sequencing technologies and assembly 97 approaches used for viral GenBank records is available in Supplement Tables S1-S6. 98 99 All rights reserved. No reuse allowed without permission.