appliedbinf / pima
Plasmid and antimicrobial resistance pipeline
☆16Updated last month
Alternatives and similar repositories for pima:
Users that are interested in pima are comparing it to the libraries listed below
- A pipeline for bioinformatics analysis of bacterial genomes☆19Updated 7 months ago
- tool to determine optimal refrerence genome given a set of fasta files☆14Updated last year
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆24Updated 10 months ago
- CFSAN Shigella Typing Pipeline☆14Updated last year
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆24Updated 4 months ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆18Updated last year
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 6 years ago
- Bacterial taxonomy construction and evaluation in R☆13Updated last year
- Static website for the PH4AGE alliance☆13Updated last year
- Interactive, web tool for exploring pan-genome of bacterial strains☆45Updated 2 years ago
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆12Updated 11 months ago
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes☆9Updated 3 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 6 years ago
- Plasmid analysis using rearrangement distances☆31Updated 3 months ago
- Calculate assocations between genes and traits☆22Updated 3 months ago
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆9Updated 3 years ago
- Hybrid Assembler for Plasmids☆10Updated 2 years ago
- Finding regions of similarity between plasmids☆16Updated 2 years ago
- plasmidVerify: plasmid contig verification tool☆12Updated 4 years ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆25Updated 2 years ago
- Predict plasmids from uncorrected long read data☆39Updated 5 years ago
- Plasmid exploration of bacterial genomes☆18Updated 2 years ago
- Get microbial sequence data easier and faster☆28Updated 5 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆56Updated last month
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- ☆13Updated 7 years ago
- ☆13Updated 3 weeks ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆22Updated 7 months ago
- Genome size estimation from long read overlaps☆48Updated 2 months ago