Repositories list

• bonphyre_pipelines

  Public
  Repository of the viral inference tool benchmark.

  Nextflow

  •

  MIT License

  •44 forks in hurwitzlab/bonphyre_pipelines•00 stars in hurwitzlab/bonphyre_pipelines•00 issues in hurwitzlab/bonphyre_pipelines•00 pull requests in hurwitzlab/bonphyre_pipelines•Updated Nov 12, 2026Nov 12, 2026

• nextflow_process_library

  Public
  Database of all the Hurwitz lab's Nextflow processes

  Nextflow

  •

  MIT License

  •00 forks in hurwitzlab/nextflow_process_library•00 stars in hurwitzlab/nextflow_process_library•00 issues in hurwitzlab/nextflow_process_library•11 pull request in hurwitzlab/nextflow_process_library•Updated Nov 12, 2026Nov 12, 2026

• containerPy

  Public
  Build reproducible, version-pinned Python/conda (conda-forge + bioconda + PyPI) Apptainer images on Hazel from a package list

  Shell

  •

  MIT License

  •00 forks in hurwitzlab/containerPy•00 stars in hurwitzlab/containerPy•00 issues in hurwitzlab/containerPy•00 pull requests in hurwitzlab/containerPy•Updated Oct 27, 2026Oct 27, 2026

• custom_containeR

  Public
  Build reproducible, version-pinned R Apptainer images on Hazel from a package list

  Shell

  •

  MIT License

  •00 forks in hurwitzlab/custom_containeR•00 stars in hurwitzlab/custom_containeR•00 issues in hurwitzlab/custom_containeR•00 pull requests in hurwitzlab/custom_containeR•Updated Oct 27, 2026Oct 27, 2026

• hpc_viral_inference_pipeline

  Public
  This directory holds the trainings and associated scripts to run the viral pipeline from https://kbase.us/n/126189/27/

  JavaScript

  •

  MIT License

  •00 forks in hurwitzlab/hpc_viral_inference_pipeline•11 star in hurwitzlab/hpc_viral_inference_pipeline•00 issues in hurwitzlab/hpc_viral_inference_pipeline•00 pull requests in hurwitzlab/hpc_viral_inference_pipeline•Updated Oct 16, 2026Oct 16, 2026

• nextflow_crash_course

  Public
  Nextflow

  •

  MIT License

  •00 forks in hurwitzlab/nextflow_crash_course•22 stars in hurwitzlab/nextflow_crash_course•00 issues in hurwitzlab/nextflow_crash_course•11 pull request in hurwitzlab/nextflow_crash_course•Updated Oct 5, 2026Oct 5, 2026

• brc_hazel_training

  Public
  Repository to share the materials from the BRZ Hazel training with the attendees.

  JavaScript

  •

  MIT License

  •00 forks in hurwitzlab/brc_hazel_training•44 stars in hurwitzlab/brc_hazel_training•00 issues in hurwitzlab/brc_hazel_training•00 pull requests in hurwitzlab/brc_hazel_training•Updated Sep 1, 2026Sep 1, 2026

• bioinfo_bonanza_2026

  Public
  Repository for the Bioinformatics Bonanza 2026 "Omics with R" sessions

  MIT License

  •00 forks in hurwitzlab/bioinfo_bonanza_2026•00 stars in hurwitzlab/bioinfo_bonanza_2026•00 issues in hurwitzlab/bioinfo_bonanza_2026•00 pull requests in hurwitzlab/bioinfo_bonanza_2026•Updated Sep 1, 2026Sep 1, 2026

• omics_with_R

  Public
  00 forks in hurwitzlab/omics_with_R•00 stars in hurwitzlab/omics_with_R•00 issues in hurwitzlab/omics_with_R•00 pull requests in hurwitzlab/omics_with_R•Updated Jul 29, 2026Jul 29, 2026

• ucd_bioinformaticscourse_2026

  Public
  Materials for the bioinformatics summer course at UC Dublin, by Mery Touceda-Suarez

  HTML

  •

  MIT License

  •00 forks in hurwitzlab/ucd_bioinformaticscourse_2026•11 star in hurwitzlab/ucd_bioinformaticscourse_2026•00 issues in hurwitzlab/ucd_bioinformaticscourse_2026•00 pull requests in hurwitzlab/ucd_bioinformaticscourse_2026•Updated Jun 18, 2026Jun 18, 2026

• metag_topic_modeling

  Public
  topic modeling approaches for metagenomics

  Jupyter Notebook

  •11 fork in hurwitzlab/metag_topic_modeling•00 stars in hurwitzlab/metag_topic_modeling•00 issues in hurwitzlab/metag_topic_modeling•00 pull requests in hurwitzlab/metag_topic_modeling•Updated Apr 8, 2026Apr 8, 2026

• vaginal_genome_assembly

  Public
  assembly for vaginal genomes from Dr. Melissa Herbst-Kralovetz

  Jupyter Notebook

  •

  MIT License

  •00 forks in hurwitzlab/vaginal_genome_assembly•00 stars in hurwitzlab/vaginal_genome_assembly•00 issues in hurwitzlab/vaginal_genome_assembly•11 pull request in hurwitzlab/vaginal_genome_assembly•Updated Nov 11, 2025Nov 11, 2025

• hurwitzlab.github.io

  Public
  Website for the Hurwitz Lab

  CSS

  •

  MIT License

  •00 forks in hurwitzlab/hurwitzlab.github.io•00 stars in hurwitzlab/hurwitzlab.github.io•00 issues in hurwitzlab/hurwitzlab.github.io•00 pull requests in hurwitzlab/hurwitzlab.github.io•Updated Oct 22, 2025Oct 22, 2025

• fmt_viruses

  Public
  detecting viruses in FMT

  Jupyter Notebook

  •

  MIT License

  •00 forks in hurwitzlab/fmt_viruses•00 stars in hurwitzlab/fmt_viruses•00 issues in hurwitzlab/fmt_viruses•00 pull requests in hurwitzlab/fmt_viruses•Updated May 23, 2025May 23, 2025

• be434-Spring2025

  Public
  Python

  •

  MIT License

  •2525 forks in hurwitzlab/be434-Spring2025•00 stars in hurwitzlab/be434-Spring2025•00 issues in hurwitzlab/be434-Spring2025•33 pull requests in hurwitzlab/be434-Spring2025•Updated May 3, 2025May 3, 2025

• install_chapel_hpc

  Public
  Shell

  •

  MIT License

  •00 forks in hurwitzlab/install_chapel_hpc•00 stars in hurwitzlab/install_chapel_hpc•00 issues in hurwitzlab/install_chapel_hpc•00 pull requests in hurwitzlab/install_chapel_hpc•Updated Apr 23, 2025Apr 23, 2025

• 2025_find_viruses

  Public
  viral pipeline

  Jupyter Notebook

  •

  MIT License

  •66 forks in hurwitzlab/2025_find_viruses•11 star in hurwitzlab/2025_find_viruses•00 issues in hurwitzlab/2025_find_viruses•00 pull requests in hurwitzlab/2025_find_viruses•Updated Apr 22, 2025Apr 22, 2025

• be487-fall-2024

  Public
  metagenomics 487/587

  Jupyter Notebook

  •00 forks in hurwitzlab/be487-fall-2024•00 stars in hurwitzlab/be487-fall-2024•00 issues in hurwitzlab/be487-fall-2024•00 pull requests in hurwitzlab/be487-fall-2024•Updated Feb 17, 2025Feb 17, 2025

• CI2025

  Public
  Applied Cyberinfrastructure course at UA

  Jupyter Notebook

  •

  MIT License

  •00 forks in hurwitzlab/CI2025•00 stars in hurwitzlab/CI2025•00 issues in hurwitzlab/CI2025•00 pull requests in hurwitzlab/CI2025•Updated Jan 27, 2025Jan 27, 2025

• biosystems-spring2025

  Public
  Python

  •

  MIT License

  •00 forks in hurwitzlab/biosystems-spring2025•00 stars in hurwitzlab/biosystems-spring2025•00 issues in hurwitzlab/biosystems-spring2025•00 pull requests in hurwitzlab/biosystems-spring2025•Updated Dec 12, 2024Dec 12, 2024

• chapel_metag_pipeline

  Public
  metagenomics workflow using chapel

  00 forks in hurwitzlab/chapel_metag_pipeline•00 stars in hurwitzlab/chapel_metag_pipeline•00 issues in hurwitzlab/chapel_metag_pipeline•00 pull requests in hurwitzlab/chapel_metag_pipeline•Updated Aug 22, 2024Aug 22, 2024

• be434-Spring2024

  Public
  Jupyter Notebook

  •

  MIT License

  •2121 forks in hurwitzlab/be434-Spring2024•00 stars in hurwitzlab/be434-Spring2024•00 issues in hurwitzlab/be434-Spring2024•00 pull requests in hurwitzlab/be434-Spring2024•Updated Apr 30, 2024Apr 30, 2024

• phage_detection_benchmarks

  Public
  Code used to benchmark metagenomic phage detection tools.

  Python

  •

  MIT License

  •11 fork in hurwitzlab/phage_detection_benchmarks•33 stars in hurwitzlab/phage_detection_benchmarks•00 issues in hurwitzlab/phage_detection_benchmarks•11 pull request in hurwitzlab/phage_detection_benchmarks•Updated Mar 3, 2024Mar 3, 2024

• Simulated_metagenomes_generator

  Public
  Pipeline to generate simulated metagenome of known composition using InSilicoSeq

  Shell

  •

  MIT License

  •00 forks in hurwitzlab/Simulated_metagenomes_generator•00 stars in hurwitzlab/Simulated_metagenomes_generator•00 issues in hurwitzlab/Simulated_metagenomes_generator•00 pull requests in hurwitzlab/Simulated_metagenomes_generator•Updated Jul 14, 2023Jul 14, 2023

• mash

  Public
  R

  •

  GNU General Public License v3.0

  •00 forks in hurwitzlab/mash•11 star in hurwitzlab/mash•00 issues in hurwitzlab/mash•22 pull requests in hurwitzlab/mash•Updated Jul 6, 2023Jul 6, 2023

• planet-microbe-functional-annotation

  Public
  Python

  •

  MIT License

  •00 forks in hurwitzlab/planet-microbe-functional-annotation•33 stars in hurwitzlab/planet-microbe-functional-annotation•00 issues in hurwitzlab/planet-microbe-functional-annotation•00 pull requests in hurwitzlab/planet-microbe-functional-annotation•Updated Jul 6, 2023Jul 6, 2023

• planet-microbe-app

  Public
  Planet Microbe - Semantic search across ‘omics, environmental, and physiochemical data layers.

  Elm

  •

  MIT License

  •33 forks in hurwitzlab/planet-microbe-app•11 star in hurwitzlab/planet-microbe-app•00 issues in hurwitzlab/planet-microbe-app•1919 pull requests in hurwitzlab/planet-microbe-app•Updated Jun 21, 2023Jun 21, 2023

• planet-microbe-semantic-web-analysis

  Public
  R

  •

  MIT License

  •00 forks in hurwitzlab/planet-microbe-semantic-web-analysis•22 stars in hurwitzlab/planet-microbe-semantic-web-analysis•00 issues in hurwitzlab/planet-microbe-semantic-web-analysis•00 pull requests in hurwitzlab/planet-microbe-semantic-web-analysis•Updated Jun 8, 2023Jun 8, 2023

• elm-imicrobe-spa

  Public
  Elm

  •

  MIT License

  •44 forks in hurwitzlab/elm-imicrobe-spa•1010 stars in hurwitzlab/elm-imicrobe-spa•00 issues in hurwitzlab/elm-imicrobe-spa•1919 pull requests in hurwitzlab/elm-imicrobe-spa•Updated Jan 7, 2023Jan 7, 2023

• b2_web

  Public
  B2 Web Interface (back/frontend)

  Elm

  •

  MIT License

  •00 forks in hurwitzlab/b2_web•00 stars in hurwitzlab/b2_web•00 issues in hurwitzlab/b2_web•66 pull requests in hurwitzlab/b2_web•Updated Dec 10, 2022Dec 10, 2022