Deep sequencing is a powerful and cost-effective tool to characterize the genetic diversity and evolution of virus populations. While modern sequencing instruments readily cover viral genomes many thousand fold and very rare variants can in principle be detected, sequencing errors, amplification biases, and other artifacts can limit sensitivity and complicate data interpretation. Here, we describe several control experiments and error correction methods for whole-genome deep sequencing of viral genomes. We developed many of these in the course of a large scale whole genome deep sequencing study of HIV-1 populations. We measured the substitution and indel errors that arose during sequencing and PCR and quantified PCR-mediated recombination. We find that depending on the viral load in the samples, rare mutations down to 0.2% can be reproducibly detected. PCR recombination can be avoided by consistently working at low amplicon concentrations.
- Downloaded 1,091 times
- Download rankings, all-time:
- Site-wide: 12,071 out of 106,159
- In genomics: 1,643 out of 6,382
- Year to date:
- Site-wide: 46,979 out of 106,159
- Since beginning of last month:
- Site-wide: 31,855 out of 106,159
Downloads over time
Distribution of downloads per paper, site-wide
- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!