katiesaund / hogwashLinks
Three bacterial GWAS methods all rolled into one easy-to-use R package
☆22Updated last year
Alternatives and similar repositories for hogwash
Users that are interested in hogwash are comparing it to the libraries listed below
Sorting:
- Phylogeny Enhanded Prediction of PAN-genome☆43Updated 5 years ago
- Bacterial GWAS analysis☆46Updated 3 weeks ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆50Updated 3 years ago
- MAG Circularization Method☆32Updated 2 weeks ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆31Updated last year
- Interactive, web tool for exploring pan-genome of bacterial strains☆48Updated 2 years ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆25Updated 6 years ago
- PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.☆62Updated 2 years ago
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆37Updated 2 months ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆42Updated 4 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- Discover and annotate the virome☆53Updated last month
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated 2 years ago
- BEAV: Bacterial Element Annotation reVamped☆72Updated 2 months ago
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆46Updated 2 years ago
- The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline☆39Updated 2 years ago
- Set of utilities on sequences and BAM files☆26Updated 4 years ago
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆24Updated 7 years ago
- strain-level analysis tools☆39Updated last year
- Gene-flank analysis tool☆33Updated 11 months ago
- Metagenomic Intra-Species Diversity Analysis (MIDAS)☆39Updated last year
- A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences☆60Updated last month
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆31Updated last month
- A pipeline for performing genome-wide association tests for bacterial genomes.☆27Updated 7 years ago
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆25Updated 3 years ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆25Updated last year
- Microbial agile accurate SNP Typer☆29Updated last year
- Gene Absence Presence Identification tool.☆27Updated 7 months ago
- Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data☆44Updated last month
- Multilocus sequence typing by blast using the schemes from PubMLST☆30Updated 3 years ago