bsmith89 / StrainFacts
Factorize metagenotypes to infer strains and their abundances
☆11Updated 3 months ago
Alternatives and similar repositories for StrainFacts:
Users that are interested in StrainFacts are comparing it to the libraries listed below
- SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.☆13Updated 2 years ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆25Updated last year
- MetaSNV, a metagenomic SNV calling pipeline.☆20Updated 2 years ago
- Metagenomic species profiling with enhanced coverage of the human gut microbiome☆25Updated 8 months ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆22Updated last year
- MiCoP is a method for high-accuracy profiling of viral and fungal metagenomic communities.☆15Updated 2 years ago
- SameStr identifies shared strains between pairs of metagenomic samples based on the similarity of SNV profiles.☆17Updated 4 months ago
- StrainFinder☆27Updated 6 years ago
- MAG Circularization Method☆33Updated 2 years ago
- Strain Prediction and Analysis with Representative SEquence☆18Updated last month
- TAXnomic Profile Aggregation and STAndardisation☆34Updated 2 months ago
- Metagenomic Estimation of Dietary Intake and Content.☆15Updated this week
- Microbial agile accurate SNP Typer☆29Updated last year
- From genomes to phenotypes: Traitar3, the microbial trait analyzer (for Python3)☆22Updated 6 months ago
- Phasing for metagenomics using PacBio long reads☆17Updated 3 years ago
- FishTaco (Functional Shifts Taxonomic Contributors) is a metagenomic computational framework that aims to identify the driver taxa of mic…☆24Updated 3 years ago
- ☆22Updated last year
- OPAL: Open-community Profiling Assessment tooL☆27Updated this week
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆25Updated 2 months ago
- Haplotype-aware genome assembly toolkit☆29Updated 5 years ago
- Analyze a set of genomes with the anvi'o pangenome pipeline☆17Updated last year
- ☆23Updated last year
- Protocols, data and code associated with the MK-SpikeSeq method for quantifying the absolute abundances of microbiota samples☆13Updated 3 years ago
- strain-level analysis tools☆33Updated 2 months ago
- Tools for extracting individual genomes from metagenomes☆17Updated last year
- Snakemake pipeline calculating KEGG orthologue abundance in metagenomic sequence data.☆24Updated 3 months ago
- Strain Resolution ON Graphs☆47Updated last year
- Improvement of metagenome-assembled genomes☆50Updated 4 years ago
- Automatic eukaryotic taxonomic classification☆28Updated 3 months ago