PopPUNK ๐จโ๐ค (POPulation Partitioning Using Nucleotide Kmers)
โ106Mar 2, 2026Updated last month
Alternatives and similar repositories for PopPUNK
Users that are interested in PopPUNK 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.โ98Mar 29, 2026Updated 2 weeks ago
- Split k-mer analysis โ version 2โ105Updated this week
- Recombination-free treesโ63Sep 1, 2025Updated 7 months ago
- Bayesian inference of ancestral dates on bacterial phylogenetic treesโ97Dec 9, 2025Updated 4 months ago
- Follow up to Grace Blackwell's 661k dataset, for 2023โ138Updated this week
- Serverless GPU API endpoints on Runpod - Bonus Credits โข AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Reorients assembled microbial sequencesโ136Aug 21, 2025Updated 7 months ago
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbinsโ216Aug 27, 2025Updated 7 months ago
- SEER, reimplemented in python ๐๐ฎโ131Mar 24, 2026Updated 3 weeks ago
- BRICK creates a BRIG-like interactive data visualisation for bacterial genome annotations and comparisonsโ21Dec 9, 2025Updated 4 months ago
- Finding regions of similarity between plasmidsโ17Nov 2, 2022Updated 3 years ago
- Pipeline for analysing intergenic regions in bacteriaโ39Oct 25, 2019Updated 6 years ago
- Plasmid analysis using rearrangement distancesโ50Updated this week
- A flexible pipeline for complete analysis of bacterial genomesโ502Updated this week
- A tool for removing redundant genomes from a set of assembliesโ79Sep 10, 2025Updated 7 months ago
- GPUs on demand by Runpod - Special Offer Available โข AdRun AI, ML, and HPC workloads on powerful cloud GPUsโwithout limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- NCBI Pathogen Detection Portal toolkitโ11Sep 6, 2023Updated 2 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignmentโ65Jun 16, 2025Updated 9 months ago
- Assemble bacterial isolate genomes from Nanopore readsโ130Jan 22, 2025Updated last year
- Library of sketching functions used by PopPUNKโ31Mar 31, 2025Updated last year
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assembliesโ173Apr 16, 2025Updated 11 months ago
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.โ148Jan 9, 2026Updated 3 months ago
- Create a tree using Mash distancesโ186Oct 24, 2023Updated 2 years ago
- โ137Mar 26, 2026Updated 2 weeks ago
- Phylogenetic compression of extremely large genome collections [661k โ๐ญ๐ฒ๐๐ถ๐ | BIGSIdata โ๐ฐ๐ด๐๐ถ๐ | AllTheBact'23 โ๐ณ๐ฑ๐๐ถ๐]โ47Apr 1, 2025Updated last year
- Managed Kubernetes at scale on DigitalOcean โข AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Split Kmer Analysisโ66May 26, 2022Updated 3 years ago
- Genomic neighbor typing of bacterial pathogens using MinHashโ42Jan 10, 2023Updated 3 years ago
- Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolatesโ86Jan 24, 2026Updated 2 months ago
- Experiments with using BIGSI data structure for metagenomic and QC applicationsโ19Aug 12, 2024Updated last year
- software to identify primers that can distinguish genomesโ20Jan 23, 2026Updated 2 months ago
- Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptopโ74Apr 1, 2026Updated last week
- pipeline for read mapping, snp calling and annotation for bacterial genomesโ13Mar 12, 2024Updated 2 years ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomesโ121May 21, 2024Updated last year
- A scalable bacterial genome assembly, annotation and analysis pipelineโ77Dec 5, 2023Updated 2 years ago
- Wordpress hosting with auto-scaling - Free Trial โข AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Fast pairwise transmission inference from single genome and/or metagenomic dataโ24Aug 1, 2025Updated 8 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 bโฆโ154Oct 2, 2025Updated 6 months ago
- Build a partitioned pangenome graph from microbial genomesโ296Mar 30, 2026Updated 2 weeks ago
- a short-read polishing tool for long-read assembliesโ211Sep 19, 2025Updated 6 months ago
- A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic dataโ70Feb 23, 2026Updated last month
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.โ13Dec 24, 2025Updated 3 months ago
- Population analysis PIPEline ๐ ๐งฌโ23Mar 2, 2026Updated last month