Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
☆41Aug 7, 2026Updated 2 months ago
Alternatives and similar repositories for mandrake
Users that are interested in mandrake are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Bifrost graph gene caller.☆102Aug 31, 2026Updated 2 months ago
- Genomic neighbor typing of bacterial pathogens using MinHash☆42Jan 10, 2023Updated 3 years ago
- Population analysis PIPEline 🛠🧬☆28Mar 2, 2026Updated 7 months ago
- taxonomic classifier based on the kraken2 algorithms and more☆46Dec 12, 2025Updated 10 months ago
- Minimum plain text representation of kmer sets☆20Jan 30, 2025Updated last year
- 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.
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆99Dec 9, 2025Updated 10 months ago
- ☆10Jun 9, 2025Updated last year
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆25Jun 17, 2022Updated 4 years ago
- Evaluating Nanopore-based bacterial variant calling☆23Oct 7, 2026Updated 3 weeks ago
- Fast tool to build the core genome of prokaryotic genomes. Can handle large datasets. Dependencis: Usearch & Numpy☆10Nov 26, 2025Updated 11 months ago
- Disty McMatrixface - compute a distance matrix from a core genome alignment file☆15Mar 15, 2023Updated 3 years ago
- ISCompare, an opensource program to identify Differentially Located Insertion Sequences☆14Apr 30, 2026Updated 6 months ago
- A pipeline for running AMRfinderPlus and collating results into functional classes☆103Updated this week
- A bioinformatic toolkit to align genome assemblies into pangenome graphs☆129Oct 14, 2026Updated 2 weeks ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Pan-genome inference and genotyping with long noisy or short accurate reads☆121Dec 13, 2024Updated last year
- Split k-mer analysis – version 2☆109Oct 20, 2026Updated last week
- Follow up to Grace Blackwell's 661k dataset, for 2023☆157Jun 10, 2026Updated 4 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆67Jun 16, 2025Updated last year
- How many distinct k-mers are there in a sequence?☆11Oct 26, 2026Updated last week
- Short-read assembler for bacterial genomics based on a de Bruijn graph written in Rust 🦅☆16Oct 20, 2026Updated last week
- Space-efficient pseudoalignment with a colored de Bruijn graph☆59Mar 13, 2025Updated last year
- Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes☆13Jun 10, 2021Updated 5 years ago
- Automated strain separation of low-complexity metagenomes☆52Nov 10, 2021Updated 4 years ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- Host depletion optimised for clinical metagenomic sequencing applications☆19Jul 9, 2026Updated 3 months ago
- Library of sketching functions used by PopPUNK☆29Jun 8, 2026Updated 4 months ago
- 🍗⭐ In silico Legionella pneumophila Sequence Based Typing☆13Feb 8, 2026Updated 8 months ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆114Oct 12, 2026Updated 2 weeks ago
- metagenome population recombination rate estimation pipeline☆12Nov 23, 2025Updated 11 months ago
- syncmer graphs, and perhaps other sorts of sequence graphs☆50Oct 13, 2026Updated 2 weeks ago
- THRESHER is a framework that replaces fixed cutoffs with data-driven phylothresholds - the SNP thresholds corrected for phylogenetic topo…☆14Oct 17, 2026Updated 2 weeks ago
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆158Jul 24, 2026Updated 3 months ago
- Graph-based assembly phasing☆102Nov 25, 2025Updated 11 months ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Fast viral consensus genome reconstruction☆27Updated this week
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆35Jul 27, 2026Updated 3 months ago
- BRICK creates a BRIG-like interactive data visualisation for bacterial genome annotations and comparisons☆22Sep 9, 2026Updated last month
- Pipeline for analysing intergenic regions in bacteria☆39Oct 25, 2019Updated 7 years ago
- Better and faster Rust implementation of the FragGeneScan gene prediction model for short and error-prone reads.☆31Feb 3, 2026Updated 8 months ago
- Scotch pipeline for indel calling.☆10Nov 25, 2019Updated 6 years ago
- ☆84Sep 13, 2023Updated 3 years ago