katholt / reddog-nf
pipeline for read mapping, snp calling and annotation for bacterial genomes
☆12Updated last year
Alternatives and similar repositories for reddog-nf:
Users that are interested in reddog-nf are comparing it to the libraries listed below
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆23Updated 8 months ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- Calculate assocations between genes and traits☆23Updated 2 weeks ago
- Microbial agile accurate SNP Typer☆29Updated last year
- Dadaist2 🟨 Highway to R☆13Updated 2 weeks ago
- ccfind - circular complete genome finder with clues of terminal redundancy☆15Updated 4 years ago
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆9Updated 4 years ago
- Finding regions of similarity between plasmids☆16Updated 2 years ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆25Updated 2 years ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆25Updated 2 years ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆44Updated 2 weeks ago
- software to identify primers that can distinguish genomes☆21Updated 2 months ago
- tool to determine optimal refrerence genome given a set of fasta files☆14Updated last year
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆24Updated 5 months ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆22Updated 2 years ago
- Bacterial taxonomy construction and evaluation in R☆13Updated last year
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 6 years ago
- ☆13Updated 7 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 6 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆19Updated 8 months ago
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆17Updated 8 months ago
- MAG Circularization Method☆33Updated 2 years ago
- Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes☆9Updated 3 years ago
- BinaRena: Interactive Visualization and Binning of Metagenomic Contigs☆31Updated 7 months ago
- Classify metagenomic contigs as eukaryotic or prokaryotic☆33Updated 2 years ago
- Plot genome alignment figure using progressiveMauve & genoPlotR☆22Updated 2 years ago
- MAGScoT - a MAG scoring and refinement tool☆32Updated 5 months ago
- SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.☆13Updated 2 years ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆27Updated 5 months ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago