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
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆25Updated 2 years ago
- Reproducible scripts and notebooks for 2019 paper on population genetics in metagenomes☆16Updated 4 years ago
- Extracts contigs harbouring a target gene / sequence from assemblies and aligns the contigs around the target sequence☆13Updated 6 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
- Structural and functional annotation of eukaryotic metagenome-assembled genomes☆21Updated last year
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- Pipeline for metagenome and metatranscriptome joint assembly☆20Updated last year
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆31Updated last year
- ☆19Updated 5 months ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Gene Absence Presence Identification tool.☆26Updated last year
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆26Updated last week
- IslandPath standalone software☆31Updated last year
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆56Updated 3 weeks ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 6 years ago
- whole genome MLST analysis☆40Updated 9 months ago
- Automatic evaluation of HGTs☆26Updated 2 weeks ago
- Phylogeny Enhanded Prediction of PAN-genome☆40Updated 4 years ago
- PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture☆32Updated 3 years ago
- Extract metadata from biosamples in NCBI☆12Updated 3 years ago
- ☆36Updated 2 years ago
- Download NCBI assembly genomes with ftp. rsync, ascp☆11Updated 2 years ago
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆23Updated 6 years ago
- Set of utilities on sequences and BAM files☆26Updated 3 years ago
- EzAAI - High Throughput Prokaryotic AAI Calculator☆38Updated 4 months ago
- Gene-flank analysis tool☆27Updated last month
- Calculate assocations between genes and traits☆22Updated 3 months ago
- Taxonomic classification of viruses at Order and Family level☆20Updated last year
- PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.☆58Updated last year
- Prophage Activity Estimator☆26Updated 8 months ago