naa a22 4500 528782436 20180924065513.0 cr unu---uuuuu 180924e20121003xx s 000 0 eng 10.3929/ethz-b-000057729 doi 10.1371/journal.pone.0047046 doi (ETHRESEARCH)oai:www.research-collection.ethz.ch:20.500.11850/57729 Read length versus Depth of Coverage for Viral Quasispecies Reconstruction [Elektronische Daten] [Osvaldo Zagordi, Martin Däumer, Christian Beisel, Niko Beerenwinkel] PLoS ONE Open access ethresearch Recent advancements of sequencing technology have opened up unprecedented opportunities in many application areas. Virus samples can now be sequenced efficiently with very deep coverage to infer the genetic diversity of the underlying virus populations. Several sequencing platforms with different underlying technologies and performance characteristics are available for viral diversity studies. Here, we investigate how the differences between two common platforms provided by 454/Roche and Illumina affect viral diversity estimation and the reconstruction of viral haplotypes. Using a mixture of ten HIV clones sequenced with both platforms and additional simulation experiments, we assessed the trade-off between sequencing coverage, read length, and error rate. For fixed costs, short Illumina reads can be generated at higher coverage and allow for detecting variants at lower frequencies. They can also be sufficient to assess the diversity of the sample if sequences are dissimilar enough, but, in general, assembly of full-length haplotypes is feasible only with the longer 454/Roche reads. The quantitative comparison highlights the advantages and disadvantages of both platforms and provides guidance for the design of viral diversity studies. Creative Commons Attribution 3.0 Unported http://creativecommons.org/licenses/by/3.0 ethresearch Zagordi Osvaldo joint author Däumer Martin joint author Beisel Christian joint author Beerenwinkel Niko joint author PLoS ONE Lawrence, Kan. : Public Library of Science 7 (10), p. e47046 1932-6203 http://hdl.handle.net/20.500.11850/57729 text/html WWW-Backlink auf das Repository (Open access) 1 Journal Article ethresearch ETHRESEARCH 856 40 http://hdl.handle.net/20.500.11850/57729 text/html WWW-Backlink auf das Repository (Open access) ETHRESEARCH 700 1- Zagordi Osvaldo joint author ETHRESEARCH 700 1- Däumer Martin joint author ETHRESEARCH 700 1- Beisel Christian joint author ETHRESEARCH 700 1- Beerenwinkel Niko joint author ETHRESEARCH 773 0- PLoS ONE Lawrence, Kan. : Public Library of Science 7 (10), p. e47046 1932-6203 BK010053 XK010053 XK010000 ETHRESEARCH ETHRESEARCH ETHRESEARCH Journal Article Open access