Contains the code and workflow for the bacterial strain definition paper with Kostas Kostantinidis
☆14Dec 4, 2023Updated 2 years ago
Alternatives and similar repositories for bacterial_strain_definition
Users that are interested in bacterial_strain_definition are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- kMetaShot is an alignment-free taxonomic classifier based on k-mer/minimizer counting for MAGs☆12Apr 27, 2026Updated 2 months ago
- HyGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors☆32Aug 26, 2024Updated last year
- Extract lineage CSVs from NCBI for use with sourmash lca.☆29Oct 4, 2023Updated 2 years ago
- Simple-to-use interactive comparison of two bacterial genomes☆28Jan 30, 2026Updated 5 months ago
- This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.☆21Mar 18, 2026Updated 4 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.
- skandiver is a program for identifying mobile genetic elements (prophages, plasmids, transposases, etc.) from assembled whole genome sequ…☆15Nov 20, 2025Updated 8 months ago
- Download assembly files from NCBI☆13May 9, 2023Updated 3 years ago
- A tool for domain based annotation with databases from the Conserved Domains Database☆30May 26, 2026Updated last month
- Snakemake template for building reusable and scalable machine learning pipelines with mikropml☆13Feb 26, 2025Updated last year
- Solving Multiple Sequence Alignment (MSA) problems with multi-objective metaheuristics☆18Jan 6, 2026Updated 6 months ago
- scripts for microbiome analysis☆12Jul 25, 2024Updated last year
- Peskas web app for East Timor☆13Jan 16, 2026Updated 6 months ago
- ☆36Nov 11, 2022Updated 3 years ago
- kmer based feature extraction tool for bioinformatics, metagenomics, AI/ML and more☆47Jul 12, 2026Updated last week
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Run and Analyse SLiM Population Genetics Forward Simulations from R.☆10Nov 26, 2025Updated 7 months ago
- UniqTag: Content-derived unique and stable identifiers for gene annotation☆10May 4, 2015Updated 11 years ago
- Prokaryotic Pangenome Analysis☆24Dec 3, 2021Updated 4 years ago
- MiGA: Microbial Genomes Atlas☆33May 26, 2026Updated last month
- ☆19May 23, 2023Updated 3 years ago
- Visualize microbial evolution at the SNP level!☆16Aug 12, 2025Updated 11 months ago
- ☆33Updated this week
- ☆17Nov 21, 2022Updated 3 years ago
- R package for fetching and parsing data of the Human Microbiome Compendium☆17May 6, 2026Updated 2 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.
- Recombination-free trees☆72Apr 26, 2026Updated 2 months ago
- WhatsGNU: a tool for identifying proteomic novelty☆16Jan 27, 2025Updated last year
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆22Apr 20, 2023Updated 3 years ago
- A manually curated database of human gut metabolic modules.☆19Jul 27, 2018Updated 7 years ago
- Personal blog website, will not update anymore. https://shixiangwang.github.io is new site☆10Aug 13, 2019Updated 6 years ago
- Paired reads mapping on de Bruijn graph☆13Jan 15, 2019Updated 7 years ago
- A pipeline for performing genome-wide association tests for bacterial genomes.☆28Apr 11, 2018Updated 8 years ago
- Analysing the genomic context of mobile genes☆11Jul 21, 2025Updated last year
- genome simulation across a population with zeta-distributed allele frequency, snps, insertions, deletions, and multi-nucleotide polymorph…☆16Mar 3, 2022Updated 4 years 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.
- A pipeline for bioinformatics analysis of bacterial genomes☆34Updated this week
- Generate de novo taxonomy of full length 16S rRNA sequences directly from environmental samples☆20Nov 23, 2024Updated last year
- sunburst plots for taxonomy - working to update Krona☆44Sep 22, 2025Updated 9 months ago
- Protocol for finding informative protein families and then using them to score metagenomic sets.☆10Oct 11, 2021Updated 4 years ago
- ☆21Updated this week
- ☆17May 22, 2026Updated last month
- ☆13Nov 28, 2018Updated 7 years ago