SameStr identifies shared strains between pairs of metagenomic samples based on the similarity of SNV profiles.
☆28Nov 19, 2025Updated 10 months ago
Alternatives and similar repositories for samestr
Users that are interested in samestr are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A repo to reproduce the experiments in the YACHT manuscript☆12Nov 2, 2023Updated 2 years ago
- A set of programs for the taxonomic analysis of genetic sequences☆15Jun 12, 2023Updated 3 years ago
- Ensemble binning strategies for combining the output of multiple binning methods.☆22Mar 11, 2023Updated 3 years ago
- MICROPHERRET: MICRObial PHEnotypic tRait ClassifieR using machine lEarning Techniques☆15Dec 16, 2025Updated 9 months ago
- ☆10Jun 9, 2025Updated last year
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- A scalable framework for automatically indexing microbial genomes and accurately characterizing metagenome-assembled genomes with Sequenc…☆24Aug 13, 2026Updated last month
- Sparse Cooccurence Network Investigation for Compositional data☆26Sep 9, 2026Updated 2 weeks ago
- StrainEst - abundance estimation of strains☆20Jan 17, 2020Updated 6 years ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆64Sep 1, 2026Updated 3 weeks ago
- Plot microbiome time series in parallel☆27Nov 7, 2023Updated 2 years ago
- Gupta et al., TaxiBGC: a Taxonomy-guided Approach for Profiling Experimentally Characterized Microbial Biosynthetic Gene Clusters and Sec…☆16May 24, 2023Updated 3 years ago
- Tool for unsupervised contig binning from viral metagenomes☆18Oct 22, 2021Updated 4 years ago
- Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes☆13Jun 10, 2021Updated 5 years ago
- Protologgger is a tool for the description of novel taxa by providing taxonomic, functional and ecological insights☆17Nov 24, 2025Updated 10 months 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.
- A tool to detect RRNPP-type quorum sensing systems☆10Mar 24, 2023Updated 3 years ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆29Feb 6, 2023Updated 3 years ago
- Teaching materials for SymbNET course: from MAGs to GEMs☆15Jan 8, 2024Updated 2 years ago
- Clustering tool optimized for sparse distance matrices: ~16M elements with ~190M connections clustered in minutes.☆16Sep 12, 2026Updated last week
- MAGinator - Accurate SNV calling and profiling of MAGs☆28Mar 23, 2026Updated 6 months ago
- Microbial Phenotype Prediction, successor to PICA, implemented with Python 3.7 and scikit-learn☆13Sep 10, 2021Updated 5 years ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆26Jul 22, 2024Updated 2 years ago
- Metaphor: a general-purpose workflow for assembly and binning of metagenomes☆40Nov 14, 2025Updated 10 months ago
- Scalable creating/updating of metagenome profiling databases☆62Jun 25, 2025Updated last year
- 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.
- Plasmid analysis using rearrangement distances☆56Jul 19, 2026Updated 2 months ago
- HOTSPOT is a hierarchical host prediction tool for plasmid contigs using Transformer.☆10Apr 22, 2024Updated 2 years ago
- Grabbing genome accessions & download info based on taxonomy, using the NCBI REST API, w00t☆12Feb 23, 2025Updated last year
- Code used to analyse and plot metadata of metagenomic binning tools☆14Aug 22, 2024Updated 2 years ago
- ☆57Sep 17, 2026Updated last week
- Accurate and robust inference of microbial growth dynamics from metagenomic sequencing☆21May 11, 2022Updated 4 years ago
- ☆18Jun 5, 2026Updated 3 months ago
- A simple script to run an alignment with nucmer and visualise its results.☆10Apr 17, 2023Updated 3 years ago
- Embedding-based indexing for compact storage and rapid querying of bacterial pan-genomes☆24Jul 11, 2026Updated 2 months 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.
- ☆20Sep 16, 2026Updated last week
- Mapping NCBI Genbank accession to GTDB accession☆14Feb 13, 2021Updated 5 years ago
- Downstream processing of VAMB binning for Viral Elucidation☆55Jul 3, 2024Updated 2 years ago
- Pipeline for metabolic annotation of microbial genomes☆155Mar 20, 2025Updated last year
- ☆17May 22, 2023Updated 3 years ago
- A comprehensive prokaryotic genome annotation pipeline☆93Sep 4, 2026Updated 2 weeks ago
- CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metage…☆235Updated this week