appliedbinf / pimaLinks
Plasmid and antimicrobial resistance pipeline
☆16Updated 9 months ago
Alternatives and similar repositories for pima
Users that are interested in pima are comparing it to the libraries listed below
Sorting:
- CFSAN Shigella Typing Pipeline☆15Updated 2 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆30Updated last week
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆19Updated 2 years ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆26Updated last year
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆26Updated 3 years ago
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆13Updated last year
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- Predict plasmids from uncorrected long read data☆40Updated 5 years ago
- Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes☆11Updated 4 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆28Updated 2 months ago
- Bacterial taxonomy construction and evaluation in R☆13Updated last year
- Interactive, web tool for exploring pan-genome of bacterial strains☆48Updated 2 years ago
- Whole genome core alignments from multiple draft genomes☆13Updated 9 years ago
- UPHL's Reference Free Pipeline☆26Updated this week
- A taxonomic classifier of plasmids☆28Updated 4 years ago
- tool to determine optimal refrerence genome given a set of fasta files☆15Updated 2 years ago
- ☆10Updated 5 months ago
- Intra-species bacterial contamination detection☆25Updated 7 months ago
- Utility to analyse a group of closely related MAgs/Genomes/bins/SUBs of more or less dubious origin☆14Updated last year
- Static website for the PH4AGE alliance☆12Updated last year
- A Nextflow pipeline designed to classify, align and assemble nanopore metagenomic reads.☆16Updated 6 months ago
- Organism-specific interpretation of AMR genotypes☆14Updated last year
- mGEMS Genomic epidemiology with mixed samples☆15Updated last year
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆62Updated 3 months ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated last year
- Metagenomic Analysis in Real Time☆28Updated 3 weeks ago
- Calculate assocations between genes and traits☆28Updated 6 months ago
- Archived - please see updated sccmec tool at link below☆13Updated last year
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆22Updated 2 years ago