A pipeline for for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets
☆32Nov 9, 2025Updated 11 months ago
Alternatives and similar repositories for ARGprofiler
Users that are interested in ARGprofiler are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆39Updated this week
- A machine learning framework to predict antibiotic resistance traits and yet unknown genes underlying resistance to specific antibiotics …☆15Oct 6, 2022Updated 4 years ago
- Simultaneous Classification and Motif Identification(eCAMI)☆11Nov 21, 2021Updated 4 years ago
- An R interface to the omixer-rpm for turning metagenomic functional profiles into pathway/module profiles☆12Dec 16, 2022Updated 3 years ago
- Processing support for Greengenes2☆15Jul 31, 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.
- BRICK creates a BRIG-like interactive data visualisation for bacterial genome annotations and comparisons☆22Sep 9, 2026Updated last month
- Antibiotic resistance genes (ARGs) have accelerated microbial threats to human health during the last decade. Here we determined the risk…☆20Apr 8, 2022Updated 4 years ago
- Altered version of PathoFact to work more conveniently with SLURM and large input files☆14Nov 7, 2024Updated last year
- ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes Detection from Metagenomic Data Using an Integrated Structured ARG Dat…☆75Aug 28, 2026Updated last month
- metagenome population recombination rate estimation pipeline☆12Nov 23, 2025Updated 10 months ago
- Ley Lab MetaGenome Profiler DataBase generator☆48Nov 9, 2022Updated 3 years ago
- Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.☆108Jan 22, 2026Updated 8 months ago
- ARGpore2☆13Oct 10, 2026Updated last week
- ☆10Jun 9, 2020Updated 6 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- ☆38Apr 15, 2024Updated 2 years ago
- A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes. It provides two models,deepARG-SS and deep…☆60Apr 30, 2026Updated 5 months ago
- A post-processing tool to reclassify Kraken 2 output based on the confidence score and/or minimum minimizer hit groups.☆11Nov 10, 2025Updated 11 months ago
- The gview wiki migrated to GitHub.☆12Sep 3, 2020Updated 6 years ago
- Contains a fasta format database of a large variety of mobile genetic elements and an annotation file☆55Aug 16, 2021Updated 5 years ago
- ☆119Updated this week
- Genomewide Epistasis Analysis on Bacteria☆15Aug 7, 2026Updated 2 months ago
- AMR++ is a bioinformatic pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resis…☆61Updated this week
- methylR: a single shiny solution from sequencer data to pathway analysis☆13Oct 30, 2024Updated last year
- 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.
- Target / Integrative Genetic Element Retriever: precisely maps IGEs (a defined type of genomic island) in bacterial and archaeal genomes;…☆20Sep 2, 2025Updated last year
- ☆12Oct 3, 2023Updated 3 years ago
- Tools for analyzing trees☆13Apr 16, 2025Updated last year
- CGView is a Java package for generating high-quality, zoomable maps of circular genomes.☆57Mar 2, 2026Updated 7 months ago
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆10Mar 10, 2026Updated 7 months ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆34Dec 4, 2025Updated 10 months ago
- Automated processing of Sanger sequencing data, taxonomic profiling, and generation of microbial strain libraries☆19Jan 4, 2026Updated 9 months ago
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates☆15Aug 26, 2024Updated 2 years ago
- A toolkit for quality control & adjustment of nucleotide redundancy in bacterial pan-genome analyses☆21Feb 12, 2026Updated 8 months 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.
- Code for paper "ToxIBTL: prediction of peptide toxicity based on information bottleneck and transfer learning"☆13Jan 24, 2022Updated 4 years ago
- A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbio…☆10Jan 23, 2026Updated 8 months ago
- Software used to develop the TCMA database associated with 10.1016/j.chom.2020.12.001.☆15Nov 26, 2023Updated 2 years ago
- A method for reconstruction of subspecies composition and functional profiles from metagenomic data☆13May 27, 2024Updated 2 years ago
- Interpretative standards for AMR genotypes☆32Oct 8, 2026Updated last week
- Gene-flank analysis tool☆37Dec 18, 2024Updated last year
- Utility to analyse a group of closely related MAgs/Genomes/bins/SUBs of more or less dubious origin☆15Sep 24, 2024Updated 2 years ago