read length versus depth of coverage for viral quasispecies reconstruction读取长度和深度覆盖病毒准物种重建.pdfVIP

Read length versus Depth of Coverage for Viral Quasispecies Reconstruction 1 ¨ 2 3 3,4 Osvaldo Zagordi , Martin Daumer , Christian Beisel , Niko Beerenwinkel * 1 Institute of Medical Virology, University of Zurich, Zurich, Switzerland, 2 Institute of Immunology and Genetics, Kaiserslautern, Germany, 3 Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland, 4 SIB Swiss Institute of Bioinformatics, Basel, Switzerland Abstract 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. ¨ Citatio