TY - JOUR
T1 - Correcting palindromes in long reads after whole-genome amplification
AU - Warris, Sven
AU - Schijlen, Elio
AU - Van De Geest, Henri
AU - Vegesna, Rahulsimham
AU - Hesselink, Thamara
AU - Te Lintel Hekkert, Bas
AU - Sanchez Perez, Gabino
AU - Medvedev, Paul
AU - Makova, Kateryna D.
AU - De Ridder, Dick
N1 - Publisher Copyright:
© 2018 The Author(s).
PY - 2018/11/6
Y1 - 2018/11/6
N2 - 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.
AB - 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.
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U2 - 10.1186/s12864-018-5164-1
DO - 10.1186/s12864-018-5164-1
M3 - Article
C2 - 30400848
AN - SCOPUS:85056263931
SN - 1471-2164
VL - 19
JO - BMC genomics
JF - BMC genomics
IS - 1
M1 - 798
ER -