A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
☆50Feb 20, 2026Updated 6 months ago
Alternatives and similar repositories for ReporTree
Users that are interested in ReporTree are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆37Updated this week
- Rapidly extract reads from FASTX files based on taxonomic classification via Kraken2.☆15Jun 17, 2026Updated 3 months ago
- Visualize microbial evolution at the SNP level!☆17Aug 12, 2025Updated last year
- A Python package to update the MLST database for the mlst tool.☆33Jul 22, 2026Updated last month
- Taxonomic Classification of Bacteria and Archaea Genomes☆19Aug 17, 2026Updated last month
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- whole genome MLST analysis☆56Jun 17, 2026Updated 3 months ago
- A taxonomic classifier of plasmids☆29Jul 7, 2021Updated 5 years ago
- Population analysis PIPEline 🛠🧬☆28Mar 2, 2026Updated 6 months ago
- 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables☆29Jun 12, 2026Updated 3 months ago
- Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure☆183Aug 10, 2026Updated last month
- ☆10Jun 9, 2025Updated last year
- BRICK creates a BRIG-like interactive data visualisation for bacterial genome annotations and comparisons☆22Sep 9, 2026Updated last week
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated 2 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆16Jun 26, 2018Updated 8 years ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Split k-mer analysis – version 2☆106Jul 9, 2026Updated 2 months ago
- Reproducible workflow for SARS-CoV-2 recombinant sequence detection.☆18May 15, 2023Updated 3 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆66Jun 16, 2025Updated last year
- Inferring global and local strict molecular clocks using root-to-tip regression☆20Jun 30, 2026Updated 2 months ago
- The MLST pipeline developed by the PathOGiST research group☆39Nov 29, 2023Updated 2 years ago
- Northern Arizona SNP Pipeline☆20Oct 29, 2024Updated last year
- ☆28Aug 2, 2023Updated 3 years ago
- Development repo for pyani-plus (the next iteration of pyani)☆36Updated this week
- Interpretative standards for AMR genotypes☆31Aug 19, 2026Updated last month
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Hierarchical clustering of cgMLST☆13Nov 20, 2023Updated 2 years ago
- Local alignment search with k-bounded matching statistics.☆24Updated this week
- Fast and space-efficient taxonomic classification of long reads☆46Jul 16, 2026Updated 2 months ago
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates☆15Aug 26, 2024Updated 2 years ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆111Jun 2, 2026Updated 3 months ago
- REcombination BARcode detector.☆17Apr 2, 2024Updated 2 years ago
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆14Jun 30, 2023Updated 3 years ago
- Recombination-free trees☆73Jul 24, 2026Updated last month
- Infer transmission clusters from SNP and timing data☆17May 20, 2020Updated 6 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- TAXnomic Profile Aggregation and STAndardisation☆45May 2, 2026Updated 4 months ago
- A pipeline for bioinformatics analysis of bacterial genomes☆34Jul 17, 2026Updated 2 months ago
- Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can b…☆158Sep 2, 2026Updated 2 weeks ago
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆13Mar 12, 2024Updated 2 years ago
- All The Bacteria CLI — query 3.2M bacterial genomes (AMR, MLST, assemblies, metadata) from the terminal☆35Sep 2, 2026Updated 2 weeks ago
- Influenza genome analysis Nextflow workflow☆28Jun 3, 2026Updated 3 months ago
- ☆10Apr 16, 2025Updated last year