strain-level analysis tools
☆41Oct 21, 2024Updated last year
Alternatives and similar repositories for StrainGE
Users that are interested in StrainGE are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers☆45Apr 8, 2024Updated 2 years ago
- MetagenOmic read Re-Assigner and abundance quantifier☆21Jun 24, 2026Updated last month
- Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes☆76Updated this week
- A pipeline to computationally identify invertible DNA regions and quantify their orientations.☆32Jan 11, 2024Updated 2 years ago
- PanTax: Strain-level metagenomic profiling using pangenome graphs☆55Jun 10, 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.
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆62Jul 31, 2026Updated 2 weeks ago
- MetaSNV, a metagenomic SNV calling pipeline.☆21Mar 25, 2022Updated 4 years ago
- A comprehensive prokaryotic genome annotation pipeline☆91Updated this week
- Fast sequence distance estimates☆30Aug 3, 2026Updated last week
- http://huttenhower.sph.harvard.edu/waafle☆24Jun 16, 2026Updated 2 months ago
- MAGinator - Accurate SNV calling and profiling of MAGs☆28Mar 23, 2026Updated 4 months ago
- Pan-genome inference and genotyping with long noisy or short accurate reads☆119Dec 13, 2024Updated last year
- Bioinformatics program inStrain☆191Mar 12, 2026Updated 5 months ago
- De novo Extraction of Strains from MetAgeNomes☆72Jun 17, 2020Updated 6 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- A hybrid assembly and MAG recovery pipeline (and more!)☆116Aug 5, 2026Updated last week
- Fast pairwise transmission inference from single genome and/or metagenomic data☆37Aug 6, 2026Updated last week
- Fast and sensitive discovery of complete phages and prophages in bacterial genome sequences☆22Dec 16, 2024Updated last year
- Strain-level abundances estimation in metagenomic samples using variation graphs☆25Jan 29, 2023Updated 3 years ago
- TAXnomic Profile Aggregation and STAndardisation☆44May 2, 2026Updated 3 months ago
- From genomes to phenotypes: Traitar3, the microbial trait analyzer (for Python3)☆21Jul 8, 2024Updated 2 years ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆70Apr 10, 2025Updated last year
- MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome☆23Nov 25, 2025Updated 8 months ago
- Analysis of the population diversity of SARS-CoV-2 within and between individual patients☆15Apr 30, 2020Updated 6 years ago
- 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.
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆28Feb 6, 2023Updated 3 years ago
- Rank homologous protein sequences based on a regressor trained on experimental measures☆16Apr 11, 2025Updated last year
- A taxonomic classifier for shotgun metagenomics reads☆11Apr 4, 2025Updated last year
- Bacterial GWAS analysis☆58Jun 12, 2026Updated 2 months ago
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆47Oct 3, 2023Updated 2 years ago
- ISCompare, an opensource program to identify Differentially Located Insertion Sequences☆14Apr 30, 2026Updated 3 months ago
- ☆24Feb 7, 2022Updated 4 years ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆40Aug 7, 2026Updated last week
- Population analysis PIPEline 🛠🧬☆26Mar 2, 2026Updated 5 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.
- detect temperate phage (active prophage) in assembled bacterial genome sequences☆15Feb 10, 2022Updated 4 years ago
- Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins for microbes or between microbes and host…☆26Jun 3, 2026Updated 2 months ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆37Apr 26, 2026Updated 3 months ago
- mGEMS Genomic epidemiology with mixed samples☆17Sep 4, 2024Updated last year
- CAMITAX: Taxon labels for microbial genomes☆31Dec 14, 2023Updated 2 years ago
- This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.☆21Mar 18, 2026Updated 4 months ago
- A simple script to run an alignment with nucmer and visualise its results.☆10Apr 17, 2023Updated 3 years ago