AMR/VF LGT focused bacterial genomics analysis workflow
☆28Feb 19, 2026Updated last month
Alternatives and similar repositories for arete
Users that are interested in arete are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆13Mar 12, 2024Updated 2 years ago
- An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.☆49Apr 20, 2023Updated 2 years ago
- This repository contains python classes and functions to quickly create a profiling tool for pathogen NGS data☆12Mar 30, 2026Updated last week
- TAXnomic Profile Aggregation and STAndardisation☆42Nov 18, 2025Updated 4 months ago
- tool to determine optimal refrerence genome given a set of fasta files☆15May 18, 2023Updated 2 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting with the flexibility to host WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Cloudways by DigitalOcean.
- Finding regions of similarity between plasmids☆17Nov 2, 2022Updated 3 years ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆35Dec 4, 2025Updated 4 months ago
- A microbial genomic analysis pipeline used by the Djordjevic Lab☆13Feb 9, 2025Updated last year
- This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.☆21Mar 18, 2026Updated 3 weeks ago
- A hybrid assembly and MAG recovery pipeline (and more!)☆106Mar 31, 2026Updated last week
- BRICK creates a BRIG-like interactive data visualisation for bacterial genome annotations and comparisons☆21Dec 9, 2025Updated 4 months ago
- Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classification☆14Apr 8, 2024Updated 2 years ago
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆18Jul 16, 2024Updated last year
- Analysing the genomic context of mobile genes☆11Jul 21, 2025Updated 8 months ago
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies☆172Apr 16, 2025Updated 11 months ago
- Bioinformatics tool for Locus Visualisation☆164Mar 30, 2026Updated last week
- 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 tool to detect acquired AMR genes directly from long read sequencing data.☆20Jan 31, 2026Updated 2 months ago
- transposable element typing pipeline☆19Mar 8, 2024Updated 2 years ago
- Pan-genome Analysis☆12May 4, 2025Updated 11 months ago
- Host depletion optimised for clinical metagenomic sequencing applications☆16Nov 18, 2024Updated last year
- MegaPath-Nano: Accurate Compositional Analysis and Drug-level Antimicrobial Resistance Detection Software for Oxford Nanopore Long-read M…☆13Jul 2, 2022Updated 3 years ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆24Aug 1, 2025Updated 8 months ago
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- Bacterial taxonomy construction and evaluation in R☆16Jan 30, 2024Updated 2 years ago
- µbinfie blog☆19Jul 21, 2025Updated 8 months ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆106Mar 2, 2026Updated last month
- A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.☆48Feb 5, 2026Updated 2 months ago
- Population analysis PIPEline 🛠🧬☆23Mar 2, 2026Updated last month
- A toolkit for quality control & adjustment of nucleotide redundancy in bacterial pan-genome analyses☆21Feb 12, 2026Updated last month
- A DRAFT, early stage book on snakemake.☆22Nov 1, 2023Updated 2 years ago
- geNomad: Identification of mobile genetic elements☆297Mar 29, 2026Updated last week
- The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…☆19May 3, 2024Updated last year
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click and start building anything your business needs.
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆39Mar 7, 2025Updated last year
- Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes☆54Oct 24, 2025Updated 5 months ago
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.☆35Dec 2, 2024Updated last year
- Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.☆106Jan 22, 2026Updated 2 months ago
- snpless-nf - A Nextflow pipeline for time-course analysis with bacterial NGS whole-genome data.☆14May 12, 2024Updated last year
- zDB: comparative bacterial genomics made easy☆40Feb 2, 2026Updated 2 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆65Jun 16, 2025Updated 9 months ago