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

doi:10.1101/173872

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

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

14 Citations (Scopus)

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 language	English
Article number	798
Journal	BMC Genomics
Volume	19
DOIs	https://doi.org/10.1101/173872 https://doi.org/10.1186/s12864-018-5164-1
Publication status	Published - 6 Nov 2018

Keywords

Chimeric reads
de novo assembly
High molecular weight DNA
Long read sequencing
Palindromes
Read mapping
Whole-genome amplification

Access to Document

10.1101/173872Licence: CC BY-ND
10.1186/s12864-018-5164-1Licence: CC BY

14 Citations
1 Software

Pacasus 1.1.1
Warris, S. (Developer), Timal, N. R. N. (Developer) & van Haarst, J. C. (Developer), 15 Jan 2018
Research output: Non-textual form › Software

Open Access

Whole-genome amplification (WGA) create specific chimeric fragments, which consist mainly of palindrome sequences. We developed the tool Pacasus to detect and correct these palindromic sequences in long reads, for example from PacBio and Nanopore
Warris, S. (Creator), Schijlen, E. G. W. M. (Creator), van de Geest, H. C. (Creator), Vegesna, R. (Creator), Hesselink, T. (Creator), te Lintel Hekkert, B. (Creator), Sanchez Perez, G. F. (Creator), Medvedev, P. (Creator), Makova, K. D. (Creator) & de Ridder, D. (Creator), Wageningen UR, 31 Jul 2017
https://www.ebi.ac.uk/ena/data/view/PRJEB21791
Dataset

Cite this

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title = "Correcting palindromes in long reads after whole-genome amplification",

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.",

keywords = "Chimeric reads, de novo assembly, High molecular weight DNA, Long read sequencing, Palindromes, Read mapping, Whole-genome amplification",

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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T1 - Correcting palindromes in long reads after whole-genome amplification

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.

KW - Chimeric reads

KW - de novo assembly

KW - High molecular weight DNA

KW - Long read sequencing

KW - Palindromes

KW - Read mapping

KW - Whole-genome amplification

U2 - 10.1101/173872

DO - 10.1101/173872

M3 - Article

SN - 1471-2164

VL - 19

JO - BMC Genomics

JF - BMC Genomics

M1 - 798

ER -

Correcting palindromes in long reads after whole-genome amplification

Abstract

Keywords

Access to Document

Fingerprint

Research output

Pacasus 1.1.1

Datasets

Whole-genome amplification (WGA) create specific chimeric fragments, which consist mainly of palindrome sequences. We developed the tool Pacasus to detect and correct these palindromic sequences in long reads, for example from PacBio and Nanopore

Cite this