NGSpeciesID: DNA barcode and amplicon consensus generation from long‐read sequencing data

Kristoffer Sahlin; Marisa C. W. Lim; Stefan Prost

doi:10.1002/ece3.7146

journal article Open Access Jan 11, 2021

NGSpeciesID: DNA barcode and amplicon consensus generation from long‐read sequencing data

Kristoffer Sahlin

Marisa C. W. Lim

Stefan Prost

Ecology and Evolution Vol. 11 No. 3 pp. 1392-1398 · Wiley

View at Publisher Save 10.1002/ece3.7146

Abstract

AbstractThird‐generation sequencing technologies, such as Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio), have gained popularity over the last years. These platforms can generate millions of long‐read sequences. This is not only advantageous for genome sequencing projects, but also advantageous for amplicon‐based high‐throughput sequencing experiments, such as DNA barcoding. However, the relatively high error rates associated with these technologies still pose challenges for generating high‐quality consensus sequences. Here, we present NGSpeciesID, a program which can generate highly accurate consensus sequences from long‐read amplicon sequencing technologies, including ONT and PacBio. The tool includes clustering of the reads to help filter out contaminants or reads with high error rates and employs polishing strategies specific to the appropriate sequencing platform. We show that NGSpeciesID produces consensus sequences with improved usability by minimizing preprocessing and software installation and scalability by enabling rapid processing of hundreds to thousands of samples, while maintaining similar consensus accuracy as current pipelines.

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References

21

[1]

Basic local alignment search tool

Stephen F. Altschul, Warren Gish, Webb Miller et al.

Journal of Molecular Biology 10.1016/s0022-2836(05)80360-2

[2]

Vertebrates on the brink as indicators of biological annihilation and the sixth mass extinction

Gerardo Ceballos, Paul R. Ehrlich, Peter H. Raven

Proceedings of the National Academy of Sciences 10.1073/pnas.1922686117

[3]

10.1186/s12859-016-0930-z

[4]

NanoPack: visualizing and processing long-read sequencing data

Wouter De Coster, Svenn D’Hert, Darrin T Schultz et al.

Bioinformatics 10.1093/bioinformatics/bty149

[5]

10.1098/rsbl.2003.0025

[6]

10.1038/nbt.4060

[7]

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

K. Katoh, D. M. Standley

Molecular Biology and Evolution 10.1093/molbev/mst010

[8]

10.1093/gigascience/giz006

[9]

10.3390/genes10110858

[10]

10.1016/j.tree.2014.10.008

[11]

10.3390/genes10060468

[12]

VSEARCH: a versatile open source tool for metagenomics

Torbjørn Rognes, Tomáš Flouri, Ben Nichols et al.

PeerJ 10.7717/peerj.2584

[13]

10.1007/978-3-030-17083-7_14

[14]

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

Patrick D. Schloss, Sarah L. Westcott, Thomas Ryabin et al.

Applied and Environmental Microbiology 10.1128/aem.01541-09

[15]

10.3390/genes11040445

[16]

10.1186/s12915-019-0706-9

[17]

10.1111/nph.14776

[18]

10.1101/gr.214270.116

[19]

10.1038/s41587-019-0217-9

[20]

10.1371/journal.pcbi.1006583

[21]

10.1111/1755-0998.12944

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Details

Published: Jan 11, 2021
Vol/Issue: 11(3)
Pages: 1392-1398
License: View

Authors

K

Kristoffer Sahlin

Department of Mathematics Science for Life Laboratory Stockholm University Stockholm Sweden

M

Marisa C. W. Lim

Department of Population Health and Reproduction University of California Davis CA USA

S

Stefan Prost

LOEWE‐Centre for Translational Biodiversity Genomics Senckenberg Frankfurt Germany; South African National Biodiversity Institute National Zoological Garden Pretoria South Africa

Cite This Article

Kristoffer Sahlin, Marisa C. W. Lim, Stefan Prost (2021). NGSpeciesID: DNA barcode and amplicon consensus generation from long‐read sequencing data. Ecology and Evolution, 11(3), 1392-1398. https://doi.org/10.1002/ece3.7146

NGSpeciesID: DNA barcode and amplicon consensus generation from long‐read sequencing data

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