Stars
app to collapse Pango lineages for reporting
Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
Geographical templates for non-contiguous cartograms of the UK.
A flexible pipeline for complete analysis of bacterial genomes
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches
Reproducible workflow for SARS-CoV-2 recombinant sequence detection.
Collection of bioinformatics training materials
Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)
InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..
Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input directory and merges everything into a single output direct…
Using ggtree to build phylogenetic trees
Web application to collect and visualise data across multiple MultiQC runs.
An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and outputs the edited (cleaned) fastq file that can safely be …
OpenABM-Covid19: an agent-based model for modelling the spread of SARS-CoV-2 (coronavirus) and control interventions for the Covid-19 epidemic
A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
Bacterial Operon Finder for Functional Organization
Tool for visualising viral lineages in space and time. As seen on covid19.sanger.ac.uk and covglobe.org.
Removal of human reads from ncov nanopore sequencing data
Collection of conceptual SVG figures created by me for talks
A place to collate notes and resources of our journey into porting nanopore sequencing over to accessible, portable technology.
snipit: summarise snps relative to your reference sequence