katholt / reddog-nfLinks
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
Sorting:
- 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
- Neptune: Genomic Signature Discovery☆20Updated 10 months ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆22Updated 2 years ago
- Finding regions of similarity between plasmids☆16Updated 2 years ago
- tool to determine optimal refrerence genome given a set of fasta files☆15Updated 2 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- Protologgger is a tool for the description of novel taxa by providing taxonomic, functional and ecological insights☆13Updated 2 years ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆26Updated last year
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆17Updated last year
- Dadaist2 🟨 Highway to R☆13Updated 6 months ago
- Resolving Species Level Classification Using Emu☆14Updated last year
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆31Updated 2 weeks ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆24Updated 2 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆46Updated 2 years ago
- ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies☆27Updated last month
- Microbial agile accurate SNP Typer☆29Updated last year
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆58Updated last year
- frame-shift correction for long-read (meta)genomics☆33Updated last year
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆27Updated 2 months ago
- Genome size estimation from long read overlaps☆61Updated 2 weeks ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆21Updated last month
- Organism-specific interpretation of AMR genotypes☆14Updated last year
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆48Updated last week
- software to identify primers that can distinguish genomes☆20Updated 7 months ago
- Utility to analyse a group of closely related MAgs/Genomes/bins/SUBs of more or less dubious origin☆14Updated 11 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 7 years ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆38Updated 6 months ago
- MiCoP is a method for high-accuracy profiling of viral and fungal metagenomic communities.☆15Updated 3 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆30Updated last week