PT  - JOURNAL ARTICLE
AU  - Sven Warris
AU  - Elio Schijlen
AU  - Henri van de Geest
AU  - Rahulsimham Vegesna
AU  - Thamara Hesselink
AU  - Bas te Lintel Hekkert
AU  - Gabino Sanchez Perez
AU  - Paul Medvedev
AU  - Kateryna D. Makova
AU  - Dick de Ridder
TI  - Correcting palindromes in long reads after whole-genome amplification
AID  - 10.1101/173872
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 173872
4099  - http://biorxiv.org/content/early/2017/08/08/173872.short
4100  - http://biorxiv.org/content/early/2017/08/08/173872.full
AB  - 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.