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

Area of Science:

• Genomics
• Bioinformatics
• Ecology

Background:

• Third-generation sequencing technologies like Oxford Nanopore Technologies (ONT) are increasingly used in ecological research due to their portability and affordability.
• While ONT excels at long-read sequencing, its application to amplicon sequencing is promising, though challenged by low raw read quality.
• Generating high-quality consensus sequences from noisy ONT amplicon data remains a significant hurdle in ecological genomics.

Purpose of the Study:

• To develop and present Amplicon_sorter, a novel bioinformatics tool.
• To enable reference-free sorting of Oxford Nanopore Technologies sequenced amplicons.
• To facilitate the construction of high-quality consensus sequences from amplicon data.

Main Methods:

• Amplicon_sorter utilizes sequence and length similarity for reference-free sorting of amplicons.
• The tool is designed to handle the specific challenges of Oxford Nanopore Technologies raw read data.
• Consensus sequence generation is a key component of the Amplicon_sorter workflow.

Main Results:

• Amplicon_sorter successfully sorts ONT-sequenced amplicons based on sequence and length.
• The tool enables the generation of robust consensus sequences from low-quality raw reads.
• Demonstrated utility in processing amplicon data for ecological applications.

Conclusions:

• Amplicon_sorter provides an effective solution for processing Oxford Nanopore Technologies amplicon sequencing data.
• The tool overcomes the challenge of low read quality to produce reliable consensus sequences.
• This facilitates the broader application of portable, low-cost sequencing in ecological research.