katholt / reddog-nfLinks
pipeline for read mapping, snp calling and annotation for bacterial genomes
☆13Updated last year
Alternatives and similar repositories for reddog-nf
Users that are interested in reddog-nf are comparing it to the libraries listed below
Sorting:
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆23Updated 2 years ago
- Neptune: Genomic Signature Discovery☆20Updated last year
- tool to determine optimal refrerence genome given a set of fasta files☆15Updated 2 years ago
- Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes☆11Updated 4 years ago
- ccfind - circular complete genome finder with clues of terminal redundancy☆15Updated 5 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆17Updated last year
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆26Updated last year
- Finding regions of similarity between plasmids☆16Updated 3 years ago
- Resolving Species Level Classification Using Emu☆14Updated last year
- ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies☆27Updated last month
- Plot genome alignment figure using progressiveMauve & genoPlotR☆22Updated 3 years ago
- A Nextflow pipeline designed to classify, align and assemble nanopore metagenomic reads.☆16Updated 8 months ago
- Microbial agile accurate SNP Typer☆29Updated last year
- Interactive, web tool for exploring pan-genome of bacterial strains☆48Updated 2 years ago
- Utility to analyse a group of closely related MAgs/Genomes/bins/SUBs of more or less dubious origin☆14Updated last year
- Fast pairwise transmission inference from single genome and/or metagenomic data☆22Updated 3 months ago
- Calculate assocations between genes and traits☆29Updated 8 months ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆27Updated 3 years ago
- Organism-specific interpretation of AMR genotypes☆14Updated last year
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆25Updated last year
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆25Updated 6 years ago
- The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…☆19Updated last year
- Bacterial taxonomy construction and evaluation in R☆14Updated last year
- frame-shift correction for long-read (meta)genomics☆33Updated last year
- Protologgger is a tool for the description of novel taxa by providing taxonomic, functional and ecological insights☆14Updated 3 weeks ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆39Updated 8 months ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆24Updated 2 years ago
- MiCoP is a method for high-accuracy profiling of viral and fungal metagenomic communities.☆15Updated 3 years ago