$ nextflow run nf-core/genomeqc
Genome quality
genomeqc
Compare the quality of many genome assemblies and their annotations in one run. Now part of nf-core, and described in a 2026 preprint.
~/work
Pipelines, projects & the path here.
I design and build reproducible Nextflow and nf-core pipelines for genomics, and use them to answer questions in evolution and ecology. Most recently I led the development ofEco-Flow, a BBSRC-funded (BB/X018768/1, £612k) programme building open-source pipelines for agri-ecology.
// pipelines
github.com/eco-flowEco-Flow pipelines
$ nextflow run eco-flow/synteny
Genome structure
synteny
Synteny analysis across genomes: trace conserved gene order and chromosome rearrangements between species.
$ nextflow run eco-flow/excon
Gene families
excon
Measure gene-family expansion and contraction across a phylogeny of species.
dietary_amplicons
Process gut COI amplicon data to work out what animals have been eating.
githubpollen-metabarcoding
Metabarcoding of pollen samples, developed in collaboration with the University of Exeter.
githubnanoporemetabarcoding
Taxonomic profiling from nanopore long-read metabarcoding data.
github// toolkit
What I work with
Languages
- Unix / Bash
- Perl
- R
- Python
- Matlab
Workflows
- Nextflow
- nf-core
- nf-test
- containers & conda
- reproducible & FAIR pipelines
Data
- RNA-Seq
- proteomics
- genomes & annotations
- phenotypic data
- metabarcoding
Analyses
- synteny
- gene-family evolution
- phylogenetics
- alternative splicing
- machine learning
// experience
full CV (pdf)The path here
- 2023 – 2026
Lead Bioinformatician, Eco-Flow
University College London · London
Lead developer and coordinator of Eco-Flow, building reproducible, nf-core-standard Nextflow pipelines for agri-ecology on the BBSRC grant “Building a Bioinformatics Ecosystem for Agri-Ecologists”.
- 2021 – 2023
Bioinformatician, Wasp Genomes Project
University College London · London
Comparative and evolutionary genomics of wasps for “The evolutionary genomics of a major transition in evolution” (NSF–NERC), with Sandra Rehan and Seirian Sumner.
- 2021
Pipeline Developer
Seqera Labs · Barcelona
Wrote Nextflow pipelines for several start-ups and contributed to the official Nextflow training material.
- 2019 – 2021
Postdoctoral Researcher
Centre for Biodiversity & Environment Research, UCL · London
Applied machine learning, transcriptomics and proteomics, with Nextflow, to wasp caste identity and evolution in the Eusocial Insect Research Group.
- 2015 – 2019
PhD in Biomedicine
Centre for Genomic Regulation (CRG) · Barcelona
Alternative splicing in early mammalian development: genome activation involves one of the most complex transcriptomes of the life cycle. Funded by a “la Caixa” fellowship.
- 2014 – 2015
MSc in Biomedical Research
Universitat Pompeu Fabra · Barcelona
Molecular and cellular pathology, cancer, immunology, genome biology and evolution.
- 2013 – 2014
Research Assistant, Evolutionary Transcriptomics
University of Bristol · Bristol
Built Perl/Unix pipelines for caste-specific brain transcriptomes and proteomes of the paper wasp Polistes canadensis.
- 2010 – 2011
MRes in Biosystematics (Distinction)
Imperial College London & Natural History Museum · London
Molecular systematics of leaf beetles, and new species of Patagonian red seaweed.