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NGSpeciesID: DNA barcode and amplicon consensus generation from long-read sequencing data
  • Kristoffer Sahlin,
  • Marisa Lim,
  • Stefan Prost
Kristoffer Sahlin
Stockholm University
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Marisa Lim
University of California Davis
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Stefan Prost
Senckenberg Research Institutes and Natural History Museums

Corresponding Author:[email protected]

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Third 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 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 
07 Oct 2020Submitted to Ecology and Evolution
13 Oct 2020Submission Checks Completed
13 Oct 2020Assigned to Editor
14 Oct 2020Reviewer(s) Assigned
11 Nov 2020Review(s) Completed, Editorial Evaluation Pending
13 Nov 2020Editorial Decision: Revise Minor
26 Nov 20201st Revision Received
27 Nov 2020Submission Checks Completed
27 Nov 2020Assigned to Editor
27 Nov 2020Review(s) Completed, Editorial Evaluation Pending
04 Dec 2020Editorial Decision: Accept