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The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/815480 doi: bioRxiv preprint The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/815480 doi: bioRxiv preprint was the most apparent. When longer read lengths were used, the variant interference PID range was much 586 narrower than when shorter read lengths were used to build contigs. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/815480 doi: bioRxiv preprint tended to be paired with Illumina more frequently compared to traditional Sanger sequencing. A small 641 number of studies even combined three or four different sequencing technologies (530 and 6 entries, 642 respectively) [Supplement Table S4 ]. Some users employed a combined approach to circumvent the inherent 643 flaws of one sequencing platform, particularly for genome finishing. 44 For example, after NGS has been used to 644 generate the majority of a RNA virus genome, RACE (Rapid amplification of cDNA ends) is typically performed 645 with Sanger to obtain the 5' or 3' termini. 45 reference-mapping assembly, the exact sequence assembly strategy used for these records is unknown, and 661 thus the contributions of both de novo assembly and reference recruitment are likely underestimated. 662 663 All rights reserved. No reuse allowed without permission.