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Next-generation Sequencing

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....

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Related Experiment Video

Updated: Jul 28, 2025

Nanopore DNA Sequencing for Metagenomic Soil Analysis

Nanopore DNA Sequencing for Metagenomic Soil Analysis

Published on: December 14, 2017

Accelerated nanopore basecalling with SLOW5 data format.

Hiruna Samarakoon^1,2,3, James M Ferguson^1,2, Hasindu Gamaarachchi^1,2,3

¹Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia.

Bioinformatics (Oxford, England)

|May 30, 2023

Summary

This summary is machine-generated.

Computational bottlenecks in nanopore sequencing basecalling are addressed by Buttery-eel. This tool leverages the SLOW5 format for faster, scalable DNA and RNA sequence generation on HPC and cloud platforms.

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Last Updated: Jul 28, 2025

Nanopore DNA Sequencing for Metagenomic Soil Analysis

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Published on: December 14, 2017

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Nanopore sequencing is a rapidly advancing genomic technology.
Computational limitations, particularly in basecalling, hinder its scalability.
Basecalling, the process of converting raw signal data to sequences, is a critical bottleneck.

Purpose of the Study:

To overcome computational constraints in nanopore sequencing.
To accelerate the basecalling process for DNA and RNA.
To enable scalable and efficient nanopore data analysis.

Main Methods:

Exploiting the SLOW5 (Slowing Down and Loading) data format for efficient sequential access.
Introducing Buttery-eel, an open-source wrapper for Oxford Nanopore's Guppy basecaller.
Integrating SLOW5 data access into the Guppy basecalling workflow.

Main Results:

Buttery-eel enables efficient sequential data access, removing analysis bottlenecks.
Significant performance improvements in nanopore basecalling were achieved.
The tool facilitates scalable and affordable basecalling on high-performance computing (HPC) and cloud environments.

Conclusions:

Buttery-eel effectively streamlines and accelerates nanopore basecalling.
The use of SLOW5 format with Buttery-eel enhances computational efficiency.
This advancement is crucial for the broader adoption and scalability of nanopore sequencing technologies.