Research group
Leggett Group
Developing new methods and tools for real-time metagenomics
Metagenomic assembly algorithms
Developing tools for assembly of metagenomic sequence data.
Group activities.
The Technology Algorithms Group is focussed on developing computational methods to enhance new sequencing technologies, particularly in the area of real-time and in-field metagenomics and surveillance.
Much of our current projects are focussed on nanopore sequencing, but we are also interested in new applications of short read technologies and other long-read technologies.
Our work usually involves software engineering, data science, algorithm development and data analysis, but members of the group are also active in the wet lab, developing DNA extraction protocols and carrying out sequencing.
Some of our current projects include:
- Developing protocols, tools, and automation for In-field and real-time sequencing.
- Developing real-time metagenomic analysis software, such as MARTi
- Development of bioinformatics tools for assembly such as the visualisation tool ALVIS or the metagenomic assembler MetaCortex.
- Detection of crop, animal and human pathogens from the air using the Air-seq pipeline.
- Clinical microbiome diagnostics: monitoring pathogens and AMR resistance in human microbiomes.
- In-field environmental sequencing.
- Ocean metagenomics.
- Viral metagenomics.
- Real-time, low-power, efficient analysis.
Projects.
Team members.
Tools.
MARTi - MARTi is a software package designed for performing real-time analysis of metagenomic samples using nanopore sequencing.
ALVIS - Alvis is a tool that can generate visualisations for a number of common long read/contig alignment analysis tasks.
NextClip - A tool for comprehensive quality analysis and read preparation for Nextera long mate pair (LMP) libraries.
NanoOK - A tool for comprehensive analysis of Oxford Nanopore MinION sequence data.
MetaCortex - A short-read metagenomic assembler.
Kontaminant - Kmer-based screening of sequencing data.
Bubbleparse - Identification of SNPs from sequencing data without a reference.
Publications.
Related reading.
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12 December 2022
Technology
FEATURE
| 10 min READ
Sky’s the limit for new air sequencing technology
There’s something in the air. Literally.
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30 January 2019
Science
FEATURE
| 5 min READ
NanoOK of the North and South: A story of life in the Antarctic
Technology and Algorithms Group Leader Dr Richard Leggett tells us about his pioneering software tools NanoOK & NanoOK RT, which are making an impact in life sciences research.
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15 April 2019
Science
FEATURE
| 5 min READ
Emma's Antarctic Adventure: Algae and climate change
Emma Langan, a PhD student in EI's Leggett group has been on a six-week expedition to Antarctica to analyse the effects of climate change on coccolithophores with real-time DNA sequencing algorithms.
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24 September 2018
Science
FEATURE
| 3 min READ
Extreme Environments: Genome sequencing & Space
Richard Leggett has recently returned from Iceland, where he’s been helping space scientists get to grips with genome sequencing in extreme environments.
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04 September 2020
Science
FEATURE
| 8 min READ
Metagenomics: exploring the unseen
Earlham Institute Scientists are at the forefront of one of biology’s modern frontiers: the untraversed depths of nature’s hidden microbial universe. From the bacteria living inside of us to the millions of single celled protists underpinning the health and prosperity of our ecosystems.
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09 July 2018
Technology
FEATURE
| 3 min READ
Real time sequencing solutions: taking the lab to the sample and beyond
With the excitement around long read DNA sequencing, what are the possibilities with nanopore technology and where is it going?
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20 April 2016
Technology
FEATURE
| 3 min READ
MinIONs, MAP and MARC: Nanotechnology developments
We're working with the latest in nanopore sequencing technology to push the boundaries of low-cost, portable genomics solutions.
07 July 2020
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What's living in the River Yare?
Rivers are the lifeblood of civilisation. It's easy to see why so many of the world's major cities were built around waterways and their fertile, alluvial plains, and Norwich is no different.
17 May 2021
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When one become two: separating DNA for more accurate nanopore analysis
A new software tool developed by Earlham Institute researchers will help bioinformaticians improve the quality and accuracy of their biological data, and avoid mis-assemblies.
21 December 2015
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NanoOK: Quality Control for portable, rapid, low-cost DNA sequencing
Scientists at the Earlham Institute (EI) have been putting Oxford Nanopore’s MinION sequencer through its paces with an open-source, sequence alignment-based genome analysis tool called ‘NanoOK’.
07 August 2019
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Where are the bees? Tracking down which flowers they pollinate
Earlham Institute researchers develop a new method to rapidly identify sources of bee pollen to understand which flowers are important for bees.
16 December 2019
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Diagnosing infections earlier in preterm babies with real time genomic analysis
Scientists at the Norwich Research Park pioneer microbiome profiling method to speed up ID of infections and more effective treatments in preterm babies.