sheppardlab / pGWAS
pGWAS and functional filtering pipeline to identify candidate adaptive genetic traits in bacteria
☆11Updated 7 years ago
Alternatives and similar repositories for pGWAS
Users that are interested in pGWAS are comparing it to the libraries listed below
Sorting:
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆25Updated 2 years ago
- Extracts contigs harbouring a target gene / sequence from assemblies and aligns the contigs around the target sequence☆13Updated 6 years ago
- Automatic evaluation of HGTs☆28Updated 3 months ago
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆24Updated 7 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆28Updated last year
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆31Updated 2 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- ☆20Updated 8 months ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆35Updated 2 weeks ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆27Updated 6 months ago
- PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture☆34Updated 3 years ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆18Updated 2 years ago
- Gene Absence Presence Identification tool.☆26Updated last month
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 6 years ago
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆21Updated 2 years ago
- Structural and functional annotation of eukaryotic metagenome-assembled genomes☆22Updated last year
- MetaGeneMark-2: Improved Gene Prediction in Metagenomes☆21Updated last year
- ☆24Updated 6 years ago
- Phylogeny Enhanded Prediction of PAN-genome☆40Updated 4 years ago
- Wrapper for the genoPlotR R package. This wrapper makes phylogeny, genbank files and blast comparisons that is needed for the genoPLotR p…☆14Updated 3 years ago
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆29Updated 3 months ago
- EzAAI - High Throughput Prokaryotic AAI Calculator☆40Updated 6 months ago
- Calculate assocations between genes and traits☆23Updated 2 months ago
- Extract metadata from biosamples in NCBI☆14Updated 4 years ago
- Prophage Activity Estimator☆26Updated 11 months ago
- whole genome MLST analysis☆42Updated last month
- Bacterial GWAS analysis☆40Updated 3 weeks ago
- Pipeline for metagenome and metatranscriptome joint assembly☆21Updated 2 years ago
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆48Updated last year
- ZGA prokaryotic genome assembly and annotation pipeline☆12Updated 8 months ago