ChrispinChaguza / RCandy
RCandy: an R package for visualising homologous recombination events in bacterial genomes
☆18Updated 2 years ago
Related projects ⓘ
Alternatives and complementary repositories for RCandy
- Gene-flank analysis tool☆26Updated 6 months ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆25Updated 2 weeks ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆24Updated 2 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…☆40Updated last week
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆25Updated 5 years ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆22Updated 3 months ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆18Updated 5 years ago
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆29Updated last year
- Plasmid analysis using rearrangement distances☆29Updated 2 months ago
- Bacterial GWAS analysis☆31Updated last month
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 3 years ago
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆25Updated last month
- IslandPath standalone software☆31Updated last year
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆24Updated last week
- Genomewide Epistasis Analysis on Bacteria☆13Updated last month
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆37Updated last month
- Automated strain separation of low-complexity metagenomes☆50Updated 3 years ago
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆41Updated last year
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆17Updated last year
- Recombination-free trees☆56Updated last year
- Microbial agile accurate SNP Typer☆29Updated 10 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆39Updated 4 months ago
- Phylogeny Enhanded Prediction of PAN-genome☆39Updated 4 years ago
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆16Updated 3 months ago
- ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies☆23Updated last year
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- Calculate assocations between genes and traits☆19Updated 2 weeks ago
- Structural and functional annotation of eukaryotic metagenome-assembled genomes☆21Updated last year
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆23Updated 6 years ago