Plasmid and antimicrobial resistance pipeline
☆16Apr 30, 2026Updated 2 months ago
Alternatives and similar repositories for pima
Users that are interested in pima are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A taxonomic classifier of plasmids☆28Jul 7, 2021Updated 5 years ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆28May 7, 2026Updated 2 months ago
- Static website for the PH4AGE alliance☆13Oct 27, 2023Updated 2 years ago
- kMetaShot is an alignment-free taxonomic classifier based on k-mer/minimizer counting for MAGs☆12Apr 27, 2026Updated 2 months ago
- Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes☆13Jun 10, 2021Updated 5 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Dryad is a Nextflow pipeline for examining prokaryote relatedness. Dryad can perform a reference free analysis and/or SNP analysis.☆20Mar 25, 2026Updated 3 months ago
- ISCompare, an opensource program to identify Differentially Located Insertion Sequences☆14Apr 30, 2026Updated 2 months ago
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates☆15Aug 26, 2024Updated last year
- PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…☆44Jul 23, 2021Updated 4 years ago
- Plot bacterial gene maps and genome comparison plots from command line with genoPlotR and GenomeDiagram☆13Mar 10, 2026Updated 4 months ago
- some useful scripts for working with genomics and sequencing data☆18Oct 31, 2019Updated 6 years ago
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.☆35Jul 11, 2026Updated last week
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆151Jul 4, 2026Updated 2 weeks ago
- An easy way of MLSTyping your genomes in R.☆19Dec 21, 2020Updated 5 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- A Python package to update the MLST database for the mlst tool.☆28May 27, 2026Updated last month
- A pipeline for bioinformatics analysis of bacterial genomes☆34Updated this week
- A curated database of completed assemblies with taxonomy IDs☆53Jun 7, 2026Updated last month
- zDB: comparative bacterial genomics made easy☆41May 6, 2026Updated 2 months ago
- A toolkit for prokaryotic comparative genomics☆52Feb 23, 2026Updated 4 months ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆22Apr 20, 2023Updated 3 years ago
- Plasmid exploration of bacterial genomes☆26Mar 2, 2022Updated 4 years ago
- A platform for targeted annotation of (meta)genomic and (meta)transcriptomic datasets using HMM sets.☆18Apr 4, 2026Updated 3 months ago
- ☆26Apr 20, 2023Updated 3 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆40Feb 20, 2026Updated 5 months ago
- Easy-to-use web application for visualization and comparison of genomes in Genbank file☆22May 27, 2022Updated 4 years ago
- 🧮 🔢 Generate multi-sample k-mer count matrix from WGS☆11Jan 17, 2026Updated 6 months ago
- Bacterial genomes finishing tool for structural insights on draft genomes☆23Sep 22, 2023Updated 2 years ago
- A tool for representing genomic potential and transcriptomic expression into KEGG pathways☆63Jul 28, 2024Updated last year
- Archived - please see updated sccmec tool at link below☆13Aug 30, 2024Updated last year
- Intra-species bacterial contamination detection☆26Jul 10, 2026Updated last week
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Feb 15, 2019Updated 7 years ago
- interactive barplot for amplicon sequencing☆13Dec 5, 2024Updated last year
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Hybrid Assembler for Plasmids☆10Jul 28, 2022Updated 3 years ago
- Bioinformatics tool to find integrons in bacterial genomes☆92May 7, 2025Updated last year
- Phigaro is a scalable command-line tool for predicting phages and prophages☆53Jan 8, 2024Updated 2 years ago
- This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.☆21Mar 18, 2026Updated 4 months ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆60Nov 3, 2023Updated 2 years ago
- Ampseer examines reads in fastq format and identifies which multiplex PCR primer set was used to generate the SARS-CoV-2 sequencing libra…☆15Feb 27, 2024Updated 2 years ago
- A toolbox for pangenome analysis and threshold evaluation.☆101Jul 8, 2022Updated 4 years ago