Correcting palindromes in long reads after whole-genome amplification

Warris, S.; Schijlen, E.G.W.M.; Geest, H.C. van de; Vegesna, R.; Hesselink, T.; Lintel Hekkert, B. te; Sanchez Perez, G.F.; Medvedev, P.; Makova, K.D.; Ridder, D. de


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.