π₯π¦π₯PHoeNIx: a platform agnostic pipeline for healthcare-associated and antimicrobial resistant pathogens
β112Sep 30, 2026Updated last week
Alternatives and similar repositories for phoenix
Users that are interested in phoenix are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- MycoSNP: Whole Genome Sequencing Analysis of Fungal Isolatesβ96Jul 23, 2026Updated 2 months ago
- UPHL's Reference Free Pipelineβ29Updated this week
- Reference-based consensus creationβ61Sep 29, 2026Updated last week
- Bacterial surveillance pipeline.β30Sep 30, 2026Updated last week
- β28Aug 2, 2023Updated 3 years ago
- 1-Click AI Models by DigitalOcean Gradient β’ AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Python Toolkit for using containerized programs in either Singularity or Dockerβ31Mar 19, 2024Updated 2 years ago
- 𧬠π» TOSTADAS β Toolkit for Open Sequence Triage, Annotation and DAtabase Submissionβ29Sep 25, 2026Updated 2 weeks ago
- A pipeline for running AMRfinderPlus and collating results into functional classesβ103Oct 2, 2026Updated last week
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.β10Jun 9, 2026Updated 4 months ago
- Spriggan is a pipeline used for assembly of bacterial whole genome sequence data and identification of antibiotic resistance genes.β16Sep 28, 2026Updated last week
- Dryad is a Nextflow pipeline for examining prokaryote relatedness. Dryad can perform a reference free analysis and/or SNP analysis.β21Updated this week
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health conβ¦β70Updated this week
- Datasets for https://github.com/nextstrain/nextcladeβ47Oct 1, 2026Updated last week
- REcombination BARcode detector.β17Apr 2, 2024Updated 2 years ago
- GPU virtual machines on DigitalOcean Gradient AI β’ AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- SC2 variant detection and composition pipelineβ19Jun 12, 2026Updated 3 months ago
- A simple pipeline for bacterial assembly and quality controlβ17Oct 1, 2026Updated last week
- Parse multiple Antimicrobial Resistance Analysis Reports into a common data structureβ182Aug 10, 2026Updated last month
- Finding regions of similarity between plasmidsβ17Jul 15, 2026Updated 2 months ago
- Bioinformatics Pipeline and Visualization resourcesβ68Aug 30, 2024Updated 2 years ago
- A Python package to update the MLST database for the mlst tool.β33Jul 22, 2026Updated 2 months ago
- Rapid determination of appropriate reference genomes.β103Jan 22, 2025Updated last year
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.β36Oct 3, 2026Updated last week
- MIRA: Portable, Interactive Application for High-Quality Influenza, SARS-CoV-2 and RSV Genome Assembly, Annotation, and Curationβ25Oct 2, 2026Updated last week
- 1-Click AI Models by DigitalOcean Gradient β’ AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.β14Jan 6, 2023Updated 3 years ago
- β10Apr 16, 2025Updated last year
- emm Automatic Isolate Labellerβ16Mar 25, 2025Updated last year
- Dockerfiles and documentation on tools for public health bioinformaticsβ226Updated this week
- QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only runβ12Dec 2, 2024Updated last year
- The R package 'phylosamp' implements novel tools that estimate the probability of transmission between two cases given phylogenetic linkaβ¦β14May 23, 2023Updated 3 years ago
- INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomiβ¦β44Updated this week
- Surveillance of pathogens using population genomics and sequencingβ62Updated this week
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolatesβ15Aug 26, 2024Updated 2 years ago
- Managed Kubernetes at scale on DigitalOcean β’ AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- β24Sep 3, 2026Updated last month
- Assembly of Nanopore Sequencingβ17Updated this week
- tool to determine optimal refrerence genome given a set of fasta filesβ15May 18, 2023Updated 3 years ago
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assembliesβ14Jun 30, 2023Updated 3 years ago
- A flexible pipeline for complete analysis of bacterial genomesβ522Aug 5, 2026Updated 2 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignmentβ67Jun 16, 2025Updated last year
- Profiling NTM WGS dataβ19Sep 1, 2026Updated last month