Correcting palindromes in long reads after whole-genome amplification

Sven Warris, Elio Schijlen, Henri Van De Geest, Rahulsimham Vegesna, Thamara Hesselink, Bas Te Lintel Hekkert, Gabino Sanchez Perez, Paul Medvedev, Kateryna D. Makova, Dick De Ridder

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

Background: 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 sequencing reads. Results: Here, we present Pacasus, a tool for correcting such errors. Two datasets show that it markedly improves read mapping and de novo assembly, yielding results similar to these that would be obtained with non-amplified DNA. Conclusions: With Pacasus long-read technologies become available for sequencing targets with very small amounts of DNA, such as single cells or even single chromosomes.

Original languageEnglish (US)
Article number798
JournalBMC genomics
Volume19
Issue number1
DOIs
StatePublished - Nov 6 2018

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Genetics

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