Correcting palindromes in long reads after whole-genome amplification
Henri van de Geest,
Bas te Lintel Hekkert,
Gabino Sanchez Perez,
Dick de Ridder
Posted 08 Aug 2017
bioRxiv DOI: 10.1101/173872 (published DOI: 10.1186/s12864-018-5164-1)
Posted 08 Aug 2017
Next-generation sequencing requires sufficient DNA to be available. If limited, whole-genome amplification is applied to generate additional amounts of DNA. Such amplification often results in many chimeric DNA fragments, in particular artificial palindromic sequences, which limit the usefulness of long reads from technologies such as PacBio and Oxford Nanopore. Here, we present Pacasus, a tool for correcting such errors in long reads. We demonstrate on two real-world datasets that it markedly improves subsequent read mapping and de novo assembly, yielding results similar to these that would be obtained with non-amplified DNA. With Pacasus long-read technologies become readily available for sequencing targets with very small amounts of DNA, such as single cells or even single chromosomes.
- Downloaded 852 times
- Download rankings, all-time:
- Site-wide: 17,909 out of 103,851
- In genomics: 2,184 out of 6,382
- Year to date:
- Site-wide: 71,163 out of 103,851
- Since beginning of last month:
- Site-wide: 55,811 out of 103,851
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!