Correcting palindromes in long reads after whole-genome amplification

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

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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.
LanguageEnglish
Article number798
JournalBMC Genomics
Volume19
DOIs
Publication statusPublished - 6 Nov 2018

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Warris, S. ; Schijlen, E.G.W.M. ; van de Geest, H.C. ; Vegesna, R. ; Hesselink, T. ; te Lintel Hekkert, B. ; Sanchez Perez, G.F. ; Medvedev, P. ; Makova, K.D. ; de Ridder, D. / Correcting palindromes in long reads after whole-genome amplification. In: BMC Genomics. 2018 ; Vol. 19.
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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.",
author = "S. Warris and E.G.W.M. Schijlen and {van de Geest}, H.C. and R. Vegesna and T. Hesselink and {te Lintel Hekkert}, B. and {Sanchez Perez}, G.F. and P. Medvedev and K.D. Makova and {de Ridder}, D.",
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Correcting palindromes in long reads after whole-genome amplification. / Warris, S.; Schijlen, E.G.W.M.; van de Geest, H.C.; Vegesna, R.; Hesselink, T.; te Lintel Hekkert, B.; Sanchez Perez, G.F.; Medvedev, P.; Makova, K.D.; de Ridder, D.

In: BMC Genomics, Vol. 19, 798, 06.11.2018.

Research output: Contribution to journalArticleAcademicpeer-review

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AU - Warris, S.

AU - Schijlen, E.G.W.M.

AU - van de Geest, H.C.

AU - Vegesna, R.

AU - Hesselink, T.

AU - te Lintel Hekkert, B.

AU - Sanchez Perez, G.F.

AU - Medvedev, P.

AU - Makova, K.D.

AU - de Ridder, D.

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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DO - 10.1101/173872

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VL - 19

JO - BMC Genomics

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JF - BMC Genomics

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