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Richard Leggett at Earlham Institute

Keywords

Metagenomics,Bioinformatics,Nanopore

Countries

United Kingdom

Activities

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Employment (7)

Earlham Institute: Norwich, Norfolk, GB

2016-11-15 to present | Technology Algorithms Group Leader
Employment
Source: Self-asserted source
Richard M. Leggett

The Genome Analysis Centre (TGAC): Norwich, Norfolk, GB

2013-03-11 to 2016-11-14 | Project Leader
Employment
Source: Self-asserted source
Richard M. Leggett

The Genome Analysis Centre (TGAC): Norwich, GB

2011-05-23 to 2013-03-10 | Postdoctoral Scientist
Employment
Source: Self-asserted source
Richard M. Leggett

Sainsbury Laboratory: Norwich, Norfolk, GB

2010-05 to 2011-05 | Postdoctoral Scientist
Employment
Source: Self-asserted source
Richard M. Leggett

University of East Anglia: Norwich, Norfolk, GB

2006-10 to 2009-07 | Associate Tutor (Computing Sciences)
Employment
Source: Self-asserted source
Richard M. Leggett

Aviva Plc Norwich: Norwich, Norfolk, GB

1998 to 2006 | Senior Systems Developer
Employment
Source: Self-asserted source
Richard M. Leggett

Acorn Computer Group: Cambridge, GB

1996 to 1998 | Software Engineer
Employment
Source: Self-asserted source
Richard M. Leggett

Education and qualifications (3)

University of East Anglia: Norwich, Norfolk, GB

2006-10 to 2010-04 | PhD Computational Biology (Computing Sciences)
Education
Source: Self-asserted source
Richard M. Leggett

University of East Anglia: Norwich, Norfolk, GB

2003-10 to 2005-09 | MSc (with Distinction) Advanced Computing Science (Computing Sciences)
Education
Source: Self-asserted source
Richard M. Leggett

University of Warwick: Coventry, Coventry, GB

1993-09 to 1996-06 | BSc (Hons) (Physics)
Education
Source: Self-asserted source
Richard M. Leggett

Funding (6)

New software for nanopore based diagnostics and surveillance

2018-07-31 to 2020-01-31 | Grant
Biotechnology and Biological Sciences Research Council (Swindon, GB)
URL: https://app.dimensions.ai/details/grant/grant.7747791
GRANT_NUMBER: BB/R022445/1
Source: Self-asserted source
Richard M. Leggett via DimensionsWizard

Computational Developments

2017-03-31 to 2020-03-30 | Grant
Biotechnology and Biological Sciences Research Council (Swindon, GB)
URL: https://app.dimensions.ai/details/grant/grant.7748095
GRANT_NUMBER: BBS/E/T/000PR9817
Source: Self-asserted source
Richard M. Leggett via DimensionsWizard

Rapid in-field Nanopore-based identification of plant and animal pathogens

2017-01-03 to 2017-03-30 | Grant
Biotechnology and Biological Sciences Research Council (Swindon, GB)
URL: https://app.dimensions.ai/details/grant/grant.6945490
GRANT_NUMBER: BBS/E/T/000GP073
Source: Self-asserted source
Richard M. Leggett via DimensionsWizard

Rapid in-field Nanopore-based identification of plant and animal pathogens

2016-06-30 to 2017-09-29 | Grant
Biotechnology and Biological Sciences Research Council (Swindon, GB)
URL: https://grants.uberresearch.com/501100000268/EBD83DE3-8D21-4A17-A50C-AB98DD561E9F/Rapid-in-field-Nanopore-based-identification-of-plant-and-animal-pathogens
GRANT_NUMBER: BB/N023196/1
Source: Self-asserted source
Richard M. Leggett via DimensionsWizard

Development of computational strategies for identification and characterisation of viruses in metagenomic samples

Source: Self-asserted source
Richard M. Leggett via DimensionsWizard
grade
Preferred source (of 2)‎

Development of computational strategies for identification and characterisation of viruses in metagenomic samples

Source: Self-asserted source
Richard M. Leggett via DimensionsWizard

Works (49)

MARTi: a real-time analysis and visualisation tool for nanopore metagenomics

2025-02-18 | Preprint
DOI: 10.1101/2025.02.14.638261
Contributors: Ned Peel; Samuel Martin; Darren Heavens; Douglas W Yu; Matthew D Clark; Richard M Leggett
Source: check_circle
Crossref

Metagenome-assembled-genomes recovered from the Arctic drift expedition MOSAiC.

Scientific data
2025-02-04 | Journal article
DOI: 10.1038/s41597-025-04525-8
PMID: 39904998
Contributors: Boulton W; Salamov A; Igor Grigoriev; Calhoun S; LaButti K; Riley R; Barry K; Fong AA; Clara Jule Marie Hoppe; Metfies K et al.
Source: Self-asserted source
Richard M. Leggett

A Comparison of Nanopore Data Types, Basecalling, and Assembly Algorithms: Whole Plant Genome Assembly and Methylation Analysis from a Single MinION Flow cell

2024-11-14 | Preprint
DOI: 10.1101/2024.11.13.623402
Contributors: Samuel Martin; Darren Heavens; Yuxuan Lan; Ned Peel; Naomi Irish; Samuel Horsfield; Michael Giolai; Matthew D. Clark; Richard M. Leggett
Source: check_circle
Crossref

Measuring air metagenomic diversity in an agricultural ecosystem.

Current biology : CB
2024-08-02 | Journal article
DOI: 10.1016/j.cub.2024.07.030
PMID: 39096906
Contributors: Giolai M; Verweij W; Martin S; Pearson N; Nicholson P; Leggett RM; Matthew Clark
Source: Self-asserted source
Richard M. Leggett

Tools for pathogen genetic surveillance: Lessons from the ash dieback invasion of Europe.

PLoS pathogens
2024-05-23 | Journal article
DOI: 10.1371/journal.ppat.1012182
PMID: 38781155
PMC: PMC11115204
Contributors: Jessica A. Peers; Leggett RM; Clark MD; Mark McMullan
Source: Self-asserted source
Richard M. Leggett

Algebraic Invariants for Inferring 4-leaf Semi-directed Phylogenetic networks

2023-09-14 | Preprint
DOI: 10.1101/2023.09.11.557152
Contributors: Samuel Martin; Vincent Moulton; Richard M. Leggett
Source: check_circle
Crossref

Dataset of 143 metagenome-assembled genomes from the Arctic and Atlantic Oceans, including 21 for eukaryotic organisms

Data in Brief
2023-02 | Journal article
DOI: 10.1016/j.dib.2023.108990
Part of ISSN: 2352-3409
Contributors: Anthony Duncan; Kerrie Barry; Chris Daum; Emiley Eloe-Fadrosh; Simon Roux; Katrin Schmidt; Susannah G. Tringe; Klaus U. Valentin; Neha Varghese; Asaf Salamov et al.
Source: Self-asserted source
Richard M. Leggett

Capturing variation in metagenomic assembly graphs with MetaCortex

Bioinformatics
2023-01-01 | Journal article
DOI: 10.1093/bioinformatics/btad020
Contributors: Samuel Martin; Martin Ayling; Livia Patrono; Mario Caccamo; Pablo Murcia; Richard M Leggett; Inanc Birol
Source: check_circle
Crossref

Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples

Genome Biology
2022-12 | Journal article
DOI: 10.1186/s13059-021-02582-x
Contributors: Samuel Martin; Darren Heavens; Yuxuan Lan; Samuel Horsfield; Matthew D. Clark; Richard M. Leggett
Source: check_circle
Crossref

Air-seq: Measuring air metagenomic diversity in an agricultural ecosystem

2022-12-15 | Preprint
DOI: 10.1101/2022.12.13.520298
Contributors: Michael Giolai; Walter Verweij; Neil Pearson; Paul Nicholson; Richard M. Leggett; Matthew D. Clark
Source: check_circle
Crossref

Multiomics in the central Arctic Ocean for benchmarking biodiversity change.

PLoS biology
2022-10-17 | Journal article
DOI: 10.1371/journal.pbio.3001835
PMID: 36251644
Contributors: Richard M. Leggett
Source: Self-asserted source
Richard M. Leggett

Plants, pollinators and their interactions under global ecological change: The role of pollen DNA metabarcoding.

Molecular ecology
2022-09-10 | Journal article
DOI: 10.1111/mec.16689
PMID: 36086900
Contributors: Richard M. Leggett
Source: Self-asserted source
Richard M. Leggett

Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans.

Microbiome
2022-04-28 | Journal article
DOI: 10.1186/s40168-022-01254-7
PMID: 35484634
PMC: PMC9047304
Contributors: Richard M. Leggett
Source: Self-asserted source
Richard M. Leggett

Alvis: a tool for contig and read ALignment VISualisation and chimera detection

BMC Bioinformatics
2021-12 | Journal article
DOI: 10.1186/s12859-021-04056-0
Contributors: Samuel Martin; Richard M. Leggett
Source: check_circle
Crossref

How low can you go? Driving down the DNA input requirements for nanopore sequencing

2021-10-18 | Other
DOI: 10.1101/2021.10.15.464554
Contributors: Darren Heavens; Darren Chooneea; Michael Giolai; Piotr Cuber; Pia Aanstad; Samuel Martin; Mark Alston; Raju Misra; Matthew D. Clark; Richard M. Leggett
Source: check_circle
Crossref

The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole.

Nature communications
2021-09-16 | Journal article
DOI: 10.1038/s41467-021-25646-9
PMID: 34531387
PMC: PMC8446083
Contributors: Richard M. Leggett
Source: Self-asserted source
Richard M. Leggett

Capturing variation in metagenomic assembly graphs with MetaCortex

2021-07-25 | Preprint
DOI: 10.1101/2021.07.23.453484
Contributors: Samuel Martin; Martin Ayling; Livia Patrono; Mario Caccamo; Pablo Murcia; Richard M. Leggett
Source: check_circle
Crossref

Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples

2021-05-08 | Preprint
DOI: 10.1101/2021.05.07.443191
Contributors: Samuel Martin; Darren Heavens; Yuxuan Lan; Samuel Horsfield; Matthew D Clark; Richard M Leggett
Source: check_circle
Crossref

Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function.

GigaScience
2020-06-01 | Journal article
DOI: 10.1093/gigascience/giaa053
PMID: 32520351
PMC: PMC7285869
Source: Self-asserted source
Richard M. Leggett

New approaches for metagenome assembly with short reads

Briefings in Bioinformatics
2020-03-23 | Journal article
DOI: 10.1093/bib/bbz020
Contributors: Martin Ayling; Matthew D Clark; Richard M Leggett
Source: check_circle
Crossref

Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens

Nature Microbiology
2019-12-16 | Journal article
DOI: 10.1038/s41564-019-0626-z
Contributors: Richard M. Leggett; Cristina Alcon-Giner; Darren Heavens; Shabhonam Caim; Thomas C. Brook; Magdalena Kujawska; Samuel Martin; Ned Peel; Holly Acford-Palmer; Lesley Hoyles et al.
Source: check_circle
Crossref

SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines.

Genome biology
2019-10-22 | Journal article
DOI: 10.1186/s13059-019-1819-8
PMID: 31639030
Source: Self-asserted source
Richard M. Leggett

Semi‐quantitative characterisation of mixed pollen samples using MinION sequencing and Reverse Metagenomics (RevMet)

Methods in Ecology and Evolution
2019-08-06 | Journal article
DOI: 10.1111/2041-210x.13265
Part of ISSN: 2041-210X
Part of ISSN: 2041-210X
Source: Self-asserted source
Richard M. Leggett

Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection.

Nature biotechnology
2019-06-24 | Journal article
DOI: 10.1038/s41587-019-0156-5
PMID: 31235920
Source: Self-asserted source
Richard M. Leggett

Alvis: a tool for contig and read ALignment VISualisation and chimera detection

2019-06-06 | Other
DOI: 10.1101/663401
Contributors: Samuel Martin; Richard M. Leggett
Source: check_circle
Crossref

New approaches for assembly of short-read metagenomic data

2018-11-08 | Other
DOI: 10.7287/peerj.preprints.27332v1
Contributors: Martin Ayling; Matthew D Clark; Richard M Leggett
Source: check_circle
Crossref

New approaches for assembly of short-read metagenomic data

2018-11-08 | Other
DOI: 10.7287/peerj.preprints.27332
Contributors: Martin Ayling; Matthew D Clark; Richard M Leggett
Source: check_circle
Crossref

Rapid Diagnosis of Lower Respiratory Infection using Nanopore-based Clinical Metagenomics

2018-08 | Other
DOI: 10.1101/387548
OTHER-ID:

PPR46788
Contributors: Charalampous T; Richardson H; Kay GL; Baldan R; Jeanes C; Rae D; Grundy S; Turner DJ; Wain J; Leggett RM et al.
Source: Self-asserted source
Richard M. Leggett via Europe PubMed Central

A world of opportunities with nanopore sequencing

Journal of Experimental Botany
2017-11-28 | Journal article
DOI: 10.1093/jxb/erx289
Contributors: Richard M Leggett; Matthew D Clark
Source: check_circle
Crossref

A world of opportunities with nanopore sequencing

2017-08-30 | Other
DOI: 10.7287/peerj.preprints.3090v2
Contributors: Richard M Leggett; Matthew D Clark
Source: check_circle
Crossref

Rapid profiling of the preterm infant gut microbiota using nanopore sequencing aids pathogen diagnostics

2017-08-24 | Preprint
DOI: 10.1101/180406
Contributors: Richard M. Leggett; Cristina Alcon-Giner; Darren Heavens; Shabhonam Caim; Thomas C. Brook; Magdalena Kujawska; Samuel Martin; Lesley Hoyles; Paul Clarke; Lindsay J. Hall et al.
Source: check_circle
Crossref

A world of opportunities with nanopore sequencing

2017-07-17 | Other
DOI: 10.7287/peerj.preprints.3090v1
Contributors: Richard M Leggett; Matthew D Clark
Source: check_circle
Crossref

MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry [version 1; referees: awaiting peer review]

2017-05-31 | Journal article
DOI: 10.12688/f1000research.11354.1
Contributors: Miten Jain; John R. Tyson; Matthew Loose; Camilla L.C. Ip; David A. Eccles; Justin O'Grady; Sunir Malla; Richard M. Leggett; Ola Wallerman; Hans J. Jansen et al.
Source: check_circle
F1000
grade
Preferred source (of 2)‎

Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data.

2015 | Journal article
DOI: 10.1371/journal.pone.0129059
PMID: 26098299
PMC: PMC4476701
Contributors: Daly GM; Leggett RM; Rowe W; Stubbs S; Wilkinson M; Ramirez-Gonzalez RH; Caccamo M; Bernal W; Heeney JL
Source: Self-asserted source
Richard M. Leggett via Europe PubMed Central

MinION Analysis and Reference Consortium: Phase 1 data release and analysis

F1000Research
2015-10 | Journal article
DOI: 10.12688/f1000research.7201.1
Part of ISSN: 2046-1402
Contributors: Camilla L.C. Ip; Matthew Loose; John R. Tyson; Mariateresa de Cesare; Bonnie L. Brown; Miten Jain; Richard M. Leggett; David A. Eccles; Vadim Zalunin; John M. Urban et al.
Source: Self-asserted source
Richard M. Leggett via Crossref Metadata Search

NanoOK: Multi-reference alignment analysis of nanopore sequencing data, quality and error profiles.

2015-09 | Journal article
PMID: 26382197
Contributors: Leggett RM; Heavens D; Caccamo M; Clark MD; Davey RP
Source: Self-asserted source
Richard M. Leggett via Europe PubMed Central

Reference-free SNP detection: dealing with the data deluge.

2014 | Journal article
DOI: 10.1186/1471-2164-15-S4-S10
PMID: 25056481
PMC: PMC4083407
Contributors: Leggett RM; MacLean D
Source: Self-asserted source
Richard M. Leggett via Europe PubMed Central

NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries.

2014-02 | Journal article
DOI: 10.1093/bioinformatics/btt702
PMID: 24297520
PMC: PMC3928519
Contributors: Leggett RM; Clavijo BJ; Clissold L; Clark MD; Caccamo M
Source: Self-asserted source
Richard M. Leggett via Europe PubMed Central

Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.

2013 | Journal article
DOI: 10.1371/journal.pone.0060058
PMID: 23536903
PMC: PMC3607606
Contributors: Leggett RM; Ramirez-Gonzalez RH; Verweij W; Kawashima CG; Iqbal Z; Jones JD; Caccamo M; Maclean D
Source: Self-asserted source
Richard M. Leggett via Europe PubMed Central

Sequencing quality assessment tools to enable data-driven informatics for high throughput genomics.

2013 | Journal article
DOI: 10.3389/fgene.2013.00288
PMID: 24381581
PMC: PMC3865868
Contributors: Leggett RM; Ramirez-Gonzalez RH; Clavijo BJ; Waite D; Davey RP
Source: Self-asserted source
Richard M. Leggett via Europe PubMed Central

StatsDB: platform-agnostic storage and understanding of next generation sequencing run metrics.

2013 | Journal article
DOI: 10.12688/f1000research.2-248.v2
PMID: 24627795
PMC: PMC3938176
Contributors: Ramirez-Gonzalez RH; Leggett RM; Waite D; Thanki A; Drou N; Caccamo M; Davey R
Source: Self-asserted source
Richard M. Leggett via Europe PubMed Central

Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations.

2013-11 | Journal article
DOI: 10.1111/tpj.12307
PMID: 23937694
PMC: PMC3935411
Contributors: Jupe F; Witek K; Verweij W; Sliwka J; Pritchard L; Etherington GJ; Maclean D; Cock PJ; Leggett RM; Bryan GJ et al.
Source: Self-asserted source
Richard M. Leggett via Europe PubMed Central

Metagenomic study of the viruses of African straw-coloured fruit bats: detection of a chiropteran poxvirus and isolation of a novel adenovirus.

2013-07 | Journal article
DOI: 10.1016/j.virol.2013.03.014
PMID: 23562481
PMC: PMC3667569
Contributors: Baker KS; Leggett RM; Bexfield NH; Alston M; Daly G; Todd S; Tachedjian M; Holmes CE; Crameri S; Wang LF et al.
Source: Self-asserted source
Richard M. Leggett via Europe PubMed Central

Coiled-coil protein Scy is a key component of a multiprotein assembly controlling polarized growth in Streptomyces.

2013-01 | Journal article
DOI: 10.1073/pnas.1210657110
PMID: 23297235
PMC: PMC3562780
Contributors: Holmes NA; Walshaw J; Leggett RM; Thibessard A; Dalton KA; Gillespie MD; Hemmings AM; Gust B; Kelemen GH
Source: Self-asserted source
Richard M. Leggett via Europe PubMed Central

Analyses of pig genomes provide insight into porcine demography and evolution.

2012-11 | Journal article
DOI: 10.1038/nature11622
PMID: 23151582
PMC: PMC3566564
Contributors: Groenen MA; Archibald AL; Uenishi H; Tuggle CK; Takeuchi Y; Rothschild MF; Rogel-Gaillard C; Park C; Milan D; Megens HJ et al.
Source: Self-asserted source
Richard M. Leggett via Europe PubMed Central

Assemblathon 1: a competitive assessment of de novo short read assembly methods.

2011-12 | Journal article
DOI: 10.1101/gr.126599.111
PMID: 21926179
PMC: PMC3227110
Contributors: Earl D; Bradnam K; St John J; Darling A; Lin D; Fass J; Yu HO; Buffalo V; Zerbino DR; Diekhans M et al.
Source: Self-asserted source
Richard M. Leggett via Europe PubMed Central

Statistical analysis of the growth and morphology of the filamentous microbe Streptomyces coelicolor

Statistical Tools for Challenges in Bioinformatics
2009 | Conference paper
Source: Self-asserted source
Richard M. Leggett

Measuring the elastomechanical properties of filamentous organisms with the calculus of variations

Systems Biology and Statistical Bioinformatics
2007 | Conference paper
Source: Self-asserted source
Richard M. Leggett

Semi-quantitative characterisation of mixed pollen samples using MinION sequencing and Reverse Metagenomics (RevMet)

Other
DOI: 10.1101/551960
Contributors: Ned Peel; Lynn Dicks; Matthew D Clark; Darren Heavens; Lawrence Percival-Alwyn; Chris Cooper; Richard G. Davies; Richard M Leggett; Douglas W Yu
Source: Self-asserted source
Richard M. Leggett via Crossref Metadata Search

Peer review (4 reviews for 4 publications/grants)

Review activity for BMC bioinformatics (1)
Review activity for Genome biology. (1)
Review activity for Microbiome (1)
Review activity for Nature biotechnology. (1)
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