pirovc / grimerLinks
GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and metadata with focus on contamination detection.
☆23Updated 2 years ago
Alternatives and similar repositories for grimer
Users that are interested in grimer are comparing it to the libraries listed below
Sorting:
- Strain-level haplotyping for metagenomes with short or long-reads.☆56Updated 7 months ago
- Microbial agile accurate SNP Typer☆29Updated last year
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated 2 years ago
- ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies☆27Updated last month
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆31Updated this week
- A taxonomic classifier of plasmids☆28Updated 4 years ago
- viralFlye pipeline☆18Updated last year
- Strain-level abundances estimation in metagenomic samples using variation graphs☆24Updated 2 years ago
- ☆24Updated 9 months ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆25Updated last year
- Neptune: Genomic Signature Discovery☆20Updated 11 months ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆35Updated 6 months ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆38Updated 8 months ago
- MetagenOmic read Re-Assigner and abundance quantifier☆18Updated 9 months ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆48Updated 2 years ago
- strain-level analysis tools☆39Updated last year
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆13Updated last year
- Intra-species bacterial contamination detection☆25Updated 9 months ago
- SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.☆13Updated 3 years ago
- frame-shift correction for long-read (meta)genomics☆33Updated last year
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- software to identify primers that can distinguish genomes☆20Updated 3 weeks ago
- Automated strain separation of low-complexity metagenomes☆52Updated 4 years ago
- Recombination-free trees☆60Updated 2 months ago
- Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets☆25Updated 3 months ago
- alignment-free coverage calculation for metagenomic binning >100 times faster☆48Updated 8 months ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆28Updated 3 months ago
- Fast and space-efficient taxonomic classification of long reads☆43Updated 2 months ago
- Calculate assocations between genes and traits☆28Updated 8 months ago