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Synteny and Rearrangement Identifier

Cython 357 38 Updated Dec 11, 2024

app to collapse Pango lineages for reporting

Python 11 1 Updated Mar 20, 2024

Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).

Python 24 1 Updated Apr 5, 2024

Geographical templates for non-contiguous cartograms of the UK.

73 12 Updated Nov 14, 2023

A flexible pipeline for complete analysis of bacterial genomes

Nextflow 428 74 Updated Nov 27, 2024

zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)

Python 51 4 Updated Dec 17, 2024

REcombination BARcode detector.

Rust 13 1 Updated Apr 2, 2024

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches

Perl 54 8 Updated Jan 22, 2025

Reproducible workflow for SARS-CoV-2 recombinant sequence detection.

Python 18 2 Updated May 15, 2023

Programmatically interact with the GISAID database.

R 72 9 Updated Sep 19, 2024

Package for creating epi-curve fishplots

R 3 1 Updated May 23, 2023

Collection of bioinformatics training materials

Python 998 184 Updated Jan 19, 2025

Systematic ProtEin AnnotatoR

Python 19 Updated Oct 17, 2024

Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)

Perl 54 19 Updated Mar 23, 2023

InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..

CSS 30 7 Updated Dec 27, 2023

Tutorial for using Singularity containers

115 12 Updated Oct 1, 2020

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…

Python 35 2 Updated May 1, 2022

Using ggtree to build phylogenetic trees

HTML 45 10 Updated Nov 6, 2024

Web application to collect and visualise data across multiple MultiQC runs.

Python 97 27 Updated Dec 13, 2024

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 …

Shell 44 8 Updated Aug 4, 2023

OpenABM-Covid19: an agent-based model for modelling the spread of SARS-CoV-2 (coronavirus) and control interventions for the Covid-19 epidemic

Python 117 75 Updated Jul 23, 2023

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019

Nextflow 91 88 Updated Nov 8, 2023

Bacterial Operon Finder for Functional Organization

Nextflow 12 1 Updated Nov 14, 2023

Tool for visualising viral lineages in space and time. As seen on covid19.sanger.ac.uk and covglobe.org.

JavaScript 10 4 Updated Jul 22, 2022

Removal of human reads from ncov nanopore sequencing data

Nextflow 5 4 Updated Mar 13, 2024

Collection of conceptual SVG figures created by me for talks

4 Updated Sep 19, 2024

A place to collate notes and resources of our journey into porting nanopore sequencing over to accessible, portable technology.

109 11 Updated May 10, 2024

snipit: summarise snps relative to your reference sequence

Python 151 28 Updated Nov 13, 2024
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