Bacterial Genomics workflow for short(Illumina) and long-read (Oxford Nanopore) sequencing data
☆12Feb 20, 2026Updated 3 months ago
Alternatives and similar repositories for bacpaq
Users that are interested in bacpaq are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- REcombination BARcode detector.☆16Apr 2, 2024Updated 2 years ago
- Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics usin…☆27Jan 30, 2025Updated last year
- Fast genealogical relationship evaluation of bacterial isolates with WGS data.☆12Jan 17, 2022Updated 4 years ago
- Archived - please see updated sccmec tool at link below☆13Aug 30, 2024Updated last year
- SISTR (Salmonella In Silico Typing Resource) command-line tool☆35Apr 24, 2025Updated last year
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆13Jun 30, 2023Updated 2 years ago
- Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.☆24Mar 7, 2026Updated 2 months ago
- In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis☆15Feb 19, 2026Updated 3 months ago
- ProkEvo - an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses.☆19Aug 16, 2021Updated 4 years ago
- A simple pipeline for bacterial assembly and quality control☆16May 14, 2026Updated 2 weeks ago
- emm Automatic Isolate Labeller☆13Mar 25, 2025Updated last year
- Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data☆188Apr 30, 2026Updated 3 weeks ago
- Influenza genome analysis Nextflow workflow☆26Mar 24, 2026Updated 2 months ago
- Build components for CloudMan, Galaxy on the Cloud, or Galaxy Server☆20Jun 27, 2017Updated 8 years ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- ☆11Mar 10, 2024Updated 2 years ago
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…☆43Jul 23, 2021Updated 4 years ago
- SeqSero2☆40Oct 1, 2025Updated 7 months ago
- Bioinformatics tool for Locus Visualisation☆166Mar 30, 2026Updated last month
- De novo clustering of long transcript reads into genes☆22Dec 15, 2025Updated 5 months ago
- a versatile toolkit for processing and analyzing diverse types of sequence data☆22May 19, 2026Updated last week
- The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.☆37Apr 13, 2024Updated 2 years ago
- ARG normalization by mapping to the ARO ontology.☆65Apr 25, 2026Updated last month
- 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.
- ☆51Apr 10, 2026Updated last month
- Python bindings for the TaxonKit library☆43Apr 6, 2026Updated last month
- A Python package to update the MLST database for the mlst tool.☆26May 22, 2026Updated last week
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated last year
- ☆10Mar 31, 2023Updated 3 years ago
- Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets☆25Apr 30, 2026Updated 3 weeks ago
- Plasmid and antimicrobial resistance pipeline☆16Apr 30, 2026Updated 3 weeks ago
- A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.☆36May 22, 2026Updated last week
- ☆17Mar 11, 2024Updated 2 years ago
- 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.
- A pipeline for taxonomic classification and functional annotation of metagenomic reads. Based on MEDUSA☆14Apr 16, 2025Updated last year
- A course in numerical methods with Python for engineers and scientists: currently 5 learning modules, with student assignments.☆10Dec 6, 2017Updated 8 years ago
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆29Aug 20, 2025Updated 9 months ago
- seqcover allows users to view coverage for hundreds of genes and dozens of samples☆51Apr 9, 2021Updated 5 years ago
- Coarse-graining library that implements Force-matching☆11Aug 31, 2020Updated 5 years ago
- ☆14Oct 29, 2024Updated last year
- Bifrost graph gene caller.☆98Apr 12, 2026Updated last month