A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
☆50Feb 20, 2026Updated 5 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:
- ☆33Updated this week
- Rapidly extract reads from FASTX files based on taxonomic classification via Kraken2.☆15Jun 17, 2026Updated last month
- Visualize microbial evolution at the SNP level!☆16Aug 12, 2025Updated 11 months ago
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated last year
- A Python package to update the MLST database for the mlst tool.☆28May 27, 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.
- Taxonomic Classification of Bacteria and Archaea Genomes☆16May 20, 2026Updated 2 months ago
- whole genome MLST analysis☆55Jun 17, 2026Updated last month
- A taxonomic classifier of plasmids☆28Jul 7, 2021Updated 5 years ago
- Population analysis PIPEline 🛠🧬☆25Mar 2, 2026Updated 4 months ago
- 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables☆29Jun 12, 2026Updated last month
- Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure☆180Apr 22, 2026Updated 2 months ago
- ☆10Jun 9, 2025Updated last year
- BRICK creates a BRIG-like interactive data visualisation for bacterial genome annotations and comparisons☆22Dec 9, 2025Updated 7 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Jun 26, 2018Updated 8 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Split k-mer analysis – version 2☆105Jul 9, 2026Updated last week
- 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☆65Jun 16, 2025Updated last year
- Inferring global and local strict molecular clocks using root-to-tip regression☆20Jun 30, 2026Updated 3 weeks ago
- The MLST pipeline developed by the PathOGiST research group☆38Nov 29, 2023Updated 2 years ago
- ☆27Aug 2, 2023Updated 2 years ago
- Development repo for pyani-plus (the next iteration of pyani)☆35Updated this week
- Interpretative standards for AMR genotypes☆30Updated this week
- Local alignment search with k-bounded matching statistics.☆24Aug 19, 2025Updated 11 months ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- Hierarchical clustering of cgMLST☆13Nov 20, 2023Updated 2 years ago
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates☆15Aug 26, 2024Updated last year
- Fast and space-efficient taxonomic classification of long reads☆45Updated this week
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆109Jun 2, 2026Updated last month
- REcombination BARcode detector.☆16Apr 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☆72Apr 26, 2026Updated 2 months ago
- Infer transmission clusters from SNP and timing data☆16May 20, 2020Updated 6 years ago
- TAXnomic Profile Aggregation and STAndardisation☆44May 2, 2026Updated 2 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- A pipeline for bioinformatics analysis of bacterial genomes☆34Updated this week
- 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…☆156Oct 2, 2025Updated 9 months 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☆33Jul 10, 2026Updated last week
- Influenza genome analysis Nextflow workflow☆27Jun 3, 2026Updated last month
- ☆10Apr 16, 2025Updated last year
- Evaluating Nanopore-based bacterial variant calling☆23Jul 23, 2025Updated 11 months ago