Overview
Collecting books is a good way to accumulate data, but you must read them to accumulate knowledge.
An inability to interpret very large datasets is one of the greatest impediments to realising the power of genomics. A primary focus of our team, together with a network of national and international collaborators, is to develop and implement software that permits a wide range of users to interpret genomic data. Software we produce is available via GitHub and published through peer reviewed journals.
Tools and Pipelines
Links to some of our tools and pipelines are provided:
This is a suite of tools packaged into a pipeline to generate complete public health microbiology reports from the raw DNA sequence reads of microorganisms of interest. It has been designed primarily for analyzing bacterial populations.
This is a software tool to rapidly annotate bacterial genome sequences.
Snippy is a DNA sequence variant finder. It takes raw DNA sequence reads from haploid organisms as an input and maps them to a reference genome to find SNPs and indels. It can compile multiple mapping outputs, compare them and create core genome and whole genome phylogenies.
This tool is used to rapidly establish the multi-locus sequence type (MLST) of your favourite bacterial pathogen. It performs in silico MLST, using a de novo assembly of a query genome sequence as input.
Like MLST, this tool takes a de novo assembly of a query genome and screens for known antibiotic resistance-associated genes.
Newcomers to genomics with a hankering for the “good ol’ days” often fret that they won’t be able to interpret older genotyping data once they switch to genomics. This fear is unfounded. Here, NG-MASTER takes genome sequence data and establishes the NG-MAST genotype for Neisseria gonorrhoea.