appliedbinf / pimaLinks
Plasmid and antimicrobial resistance pipeline
☆16Updated last year
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☆32Updated 2 weeks ago
- ☆10Updated 9 months ago
- Organism-specific interpretation of AMR genotypes☆15Updated last year
- Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes☆13Updated 4 years ago
- Static website for the PH4AGE alliance☆13Updated 2 years ago
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆13Updated last year
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆20Updated 2 years ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆26Updated last year
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆28Updated 6 months ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆27Updated 3 years ago
- Intra-species bacterial contamination detection☆25Updated this week
- Whole genome core alignments from multiple draft genomes☆13Updated 9 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- tool to determine optimal refrerence genome given a set of fasta files☆15Updated 2 years ago
- A taxonomic classifier of plasmids☆28Updated 4 years ago
- Order and orientation of complete bacterial genomes☆29Updated 6 months ago
- Predict plasmids from uncorrected long read data☆41Updated 3 months ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆48Updated 3 weeks ago
- Finding regions of similarity between plasmids☆17Updated 3 years ago
- A Nextflow pipeline designed to classify, align and assemble nanopore metagenomic reads.☆17Updated 10 months ago
- Bacterial taxonomy construction and evaluation in R☆15Updated 2 years ago
- UPHL's Reference Free Pipeline☆27Updated 3 months ago
- Interpretative standards for AMR genotypes☆27Updated this week
- Fast pairwise transmission inference from single genome and/or metagenomic data☆23Updated 6 months ago
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆10Updated 4 months ago
- Perform taxonomic profiling analyses for long-read shotgun metagenomic datasets. Developed for the Long Read Sequencing Workshop 2022 at …☆13Updated 3 years ago
- Colinear block visualisation tool☆31Updated 2 years ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆39Updated 11 months ago
- Predict MLST directly from uncorrected long reads☆27Updated 3 months ago