cimendes / roProfile
Generation of pan-genome profile files using Roary output.
☆9Updated 7 years ago
Related projects ⓘ
Alternatives and complementary repositories for roProfile
- Plasmid and antimicrobial resistance pipeline☆16Updated last year
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆11Updated 8 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆37Updated 2 months ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆18Updated 5 years ago
- Predict MLST directly from uncorrected long reads☆25Updated 2 years ago
- Colinear block visualisation tool☆30Updated 9 months ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆24Updated 7 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 6 years ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…☆40Updated 2 weeks ago
- ☆14Updated last year
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆22Updated 3 months ago
- A pipeline for bioinformatics analysis of bacterial genomes☆19Updated 4 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆40Updated 4 months ago
- Plasmid exploration of bacterial genomes☆17Updated 2 years ago
- Reproducible scripts and notebooks for 2019 paper on population genetics in metagenomes☆15Updated 4 years ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆24Updated 2 years ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆25Updated 3 weeks ago
- Microbial agile accurate SNP Typer☆29Updated 10 months ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆17Updated last year
- viralFlye pipeline☆19Updated 3 months ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆22Updated last month
- Intra-species bacterial contamination detection☆22Updated last year
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆9Updated 3 years ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆25Updated 5 years ago
- tool to determine optimal refrerence genome given a set of fasta files☆14Updated last year
- Interactive, web tool for exploring pan-genome of bacterial strains☆44Updated last year
- MAGScoT - a MAG scoring and refinement tool☆28Updated last month
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆29Updated last year
- Finding regions of similarity between plasmids☆16Updated 2 years ago