wanyuac / GeneMates
An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences
☆25Updated 2 years ago
Alternatives and similar repositories for GeneMates:
Users that are interested in GeneMates are comparing it to the libraries listed below
- pGWAS and functional filtering pipeline to identify candidate adaptive genetic traits in bacteria☆11Updated 7 years ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆18Updated last year
- ☆20Updated 7 months ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Extracts contigs harbouring a target gene / sequence from assemblies and aligns the contigs around the target sequence☆13Updated 6 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 6 years ago
- Calculate assocations between genes and traits☆23Updated last month
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆28Updated last year
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆27Updated 2 months ago
- whole genome MLST analysis☆41Updated 2 weeks ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆33Updated last month
- Structural and functional annotation of eukaryotic metagenome-assembled genomes☆22Updated last year
- ☆13Updated 7 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆59Updated last month
- Gene Absence Presence Identification tool.☆26Updated 2 weeks ago
- Extract metadata from biosamples in NCBI☆13Updated 4 years ago
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆48Updated 11 months ago
- This repository contains R code for building a heatmap and histogram with the output of FastANI☆16Updated 3 years ago
- EzAAI - High Throughput Prokaryotic AAI Calculator☆39Updated 6 months ago
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆24Updated 6 years ago
- ☆25Updated last year
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆21Updated 2 years ago
- This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.☆20Updated last year
- Find Prokaryotic DNA methylase genes in proteins, contigs, or genomes☆11Updated 10 months ago
- Reproducible scripts and notebooks for 2019 paper on population genetics in metagenomes☆16Updated 5 years ago
- PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture☆33Updated 3 years ago
- Plasmid exploration of bacterial genomes☆18Updated 3 years ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆27Updated 5 months ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆21Updated 6 months ago
- Gene-flank analysis tool☆27Updated 3 months ago