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Amplicon_sorter: a tool for reference-free amplicon sorting based on sequence similarity and for building consensus sequences

Citation

Vierstraete, Andy; Braeckman, Bart (2022), Amplicon_sorter: a tool for reference-free amplicon sorting based on sequence similarity and for building consensus sequences, Dryad, Dataset, https://doi.org/10.5061/dryad.zgmsbccd0

Abstract

Oxford Nanopore Technologies (ONT) is a third-generation sequencing technology that is gaining popularity in ecological research for its portable and low-cost sequencing possibilities. Although the technology excels at long-read sequencing, it can also be applied to sequence amplicons. The downside of ONT is the low quality of the raw reads. Hence, generating a high-quality consensus sequence is still a challenge. We present Amplicon_sorter, a tool for reference-free sorting of ONT sequenced amplicons based on their similarity in sequence and length and for building solid consensus sequences.

Methods

Oxford Nanopore sequencing was done on a 9.4.1 MinION Flow cell and basecalling was done in Guppy 4.2.2 (HAC) and Guppy 5.0.7 (supHAC).

Usage Notes

Amplicon_sorter: a tool for reference-free amplicon sorting based on sequence similarity and for building consensus sequences

Andy Vierstraete*, Bart P. Braeckman

Laboratory of aging physiology and Molecular Evolution, University of Gent, 9000 Gent, Belgium

andy.vierstraete@ugent.be

These data files were used for the above publication.

  • Barcode_sequences.xlsx: contains the sequence of the different barcodes.
  • Barcodes_species.xlsx: list of species and their corresponding barcodes.
  • Sanger_references.fasta: the sanger references of the used species.
  • HAC_data.zip: the fastq file basecalled with the High Accuracy option in Guppy.
  • supHAC_data.zip: the fastq file basecalled with the Super Accuracy option in Guppy.

The data files contain more barcodes and data than used in the publication.  The testrun was combined with samples from another lab that is working with fungi. 

Funding