Infer transmission clusters from SNP and timing data
☆16May 20, 2020Updated 5 years ago
Alternatives and similar repositories for transcluster
Users that are interested in transcluster are comparing it to the libraries listed below
Sorting:
- A snakemake workflow for WGS-based tuberculosis transmission analysis☆19Dec 3, 2024Updated last year
- Population analysis PIPEline 🛠🧬☆22Feb 3, 2026Updated 3 weeks ago
- ☆38Apr 14, 2022Updated 3 years ago
- A microbial genomic analysis pipeline used by the Djordjevic Lab☆13Feb 9, 2025Updated last year
- Gene Absence Presence Identification tool.☆27Mar 28, 2025Updated 11 months ago
- Quickly generate consensus assemblies for bacterial genomes☆14Sep 12, 2025Updated 5 months ago
- 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables☆29Feb 12, 2026Updated 2 weeks ago
- snpless-nf - A Nextflow pipeline for time-course analysis with bacterial NGS whole-genome data.☆14May 12, 2024Updated last year
- Mutual nearest neighbor graphs for population structure inference and visualization☆18Dec 4, 2025Updated 2 months ago
- zDB: comparative bacterial genomics made easy☆38Feb 2, 2026Updated last month
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆39Mar 7, 2025Updated 11 months ago
- Reconstruction of transmission trees using genomic data☆72Sep 27, 2023Updated 2 years ago
- A bacterial GWAS pipeline written in Nextflow that uses Pyseer; Part III Project for Systems Biology at the University of Cambridge☆21Jan 20, 2026Updated last month
- A library of Machine Learning tools to predict antibiotic resistance from NGS data☆18May 30, 2022Updated 3 years ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆47Feb 20, 2026Updated last week
- Phylodynamic inference☆21May 15, 2020Updated 5 years ago
- transposable element typing pipeline☆19Mar 8, 2024Updated last year
- Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure☆173Updated this week
- ☆20Jan 23, 2019Updated 7 years ago
- Three bacterial GWAS methods all rolled into one easy-to-use R package☆22Apr 16, 2024Updated last year
- ☆20Nov 18, 2021Updated 4 years ago
- All scripts used for the analysis of the twilight of the pan-genome, and scripts available for others to apply similar analysis☆19Mar 30, 2021Updated 4 years ago
- This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.☆21May 16, 2023Updated 2 years ago
- Within-species genome-wide dN/dS estimation from very many genomes☆23Oct 26, 2020Updated 5 years ago
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆95Dec 9, 2025Updated 2 months ago
- Genome comparison via de Bruijn graph. To get the latest stable version, please visit our site.☆69Oct 29, 2020Updated 5 years ago
- Plascad is a computationally efficient tool designed for plasmids classification, antibiotic resistance genes (ARGs) annotation and plasm…☆51Feb 2, 2021Updated 5 years ago
- AMR/VF LGT focused bacterial genomics analysis workflow☆28Feb 19, 2026Updated last week
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆29Jul 18, 2025Updated 7 months ago
- A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data☆68Feb 23, 2026Updated last week
- Library of sketching functions used by PopPUNK☆31Mar 31, 2025Updated 11 months ago
- Predict MLST directly from uncorrected long reads☆27Oct 31, 2025Updated 4 months ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆27Aug 8, 2022Updated 3 years ago
- ☆36Dec 22, 2025Updated 2 months ago
- post processing of bacterial pangenome gene presence/absence matrices☆64Jan 19, 2026Updated last month
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆65Jun 16, 2025Updated 8 months ago
- Detection and classification selective sweep use domain adaptive model☆10Apr 29, 2024Updated last year
- Locus and lineage tests for bacterial GWAS☆28Oct 5, 2017Updated 8 years ago
- A genome diagram generator for microbes and organelles☆57Updated this week