Parasites and Microbes
This currently includes the following activities:
- Development and maintenance of automated pipelines for tracking and analysis of sequencing data
- Development of open-source software tools for downstream analysis of genomic data, such as Artemis, Roary, or Ariba
- Ad-hoc informatics support to members of the programme via a helpdesk
- Bioinformatics training courses for in-house scientists and the wider community
- Maintenance of websites that make genomic data and research findings available to the community, such as GeneDB
- Development of a platform for community genome annotation
Dr Christoph Puethe
Senior Scientific Manager
Christoph joined the Sanger Institute in 2018 as a software developer. In 2019 took on the role of managing the Pathogen Informatics team, which provides informatics support to the Parasites and Microbes programme. Christoph has a PhD in geophysics from ETH Zurich and working experience as software developer both in academia and industry.
A software application that identifies anitbiotic resistance genes by running local assemblies.
Artemis Comparison Tool (ACT)
ACT is a Java application for displaying pairwise comparisons between two or more DNA sequences.
An interactive Java application for generating circular and linear representations of genomes.
A genome database containing the latest sequence data and annotation/curation for organisms sequenced by the Pathogen group.
Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) can be used to identify recombination.
A de novo assembler designed specifically for read pairs sequenced at highly variable depth from RNA virus samples.
A software application for taking MLST databases from multiple locations and consolidating them in one place so that they can ...
A software application for rapidly constructing pan genomes from large numbers of prokaryote samples.
A software application for fast, reference-free pseudo-phylogenomic trees from reads or contigs.
Genomic Epidemiology of Infectious Diseases
Our mission is to inform control strategies and interventions on a local, national and international scale. Our group consists of a ...
The Parasite Genomics group uses comparative and functional genomics approaches to investigate the biology of helminths and protozoan parasites.
Genomics of Pneumonia and Meningitis (and neonatal sepsis)
Parasites and Microbes
We study variation in the genomes of major bacterial pathogens to understand their evolution in the context of disease and asymptomatic ...
The host-microbiota Interactions laboratory studies the mechanisms that underlie how micro-organisms in the gut, nasopharynx and uro-gential tract interact with their ...
The Microbial Pathogenesis team, under the leadership of Professor Gordon Dougan, focused on the genetic analysis of the interactions between ...
The aim of the Virus Genomics team was to understand how genetic changes in viruses and hosts influence the biological ...