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    99 repositories

    • workflows-nextflow

      Public
      Workflow management with Nextflow and nf-core
      Nextflow
      •
      Other
      •40•0•0•0•Updated Feb 3, 2026Feb 3, 2026

    • hpcbio-swc-shell-novice-sp2025

      Public
      Shell
      •
      Other
      •0•0•0•0•Updated Feb 3, 2026Feb 3, 2026

    • configs

      Public
      Config files used to define parameters specific to compute environments at different Institutions
      Nextflow
      •
      MIT License
      •339•0•0•1•Updated Jan 24, 2026Jan 24, 2026

    • TADA

      Public
      TADA - Targeted Amplicon Diversity Analysis - a DADA2-focused Nextflow workflow for any targeted amplicon region
      Nextflow
      •
      MIT License
      •15•22•25•0•Updated Dec 11, 2025Dec 11, 2025

    • hpcbio-swc-bioc-intro

      Public
      R
      •
      Other
      •0•0•0•1•Updated Dec 2, 2025Dec 2, 2025

    • eASV-pipeline-for-515Y-926R

      Public
      This is a collection of scripts for analyzing mixed 16S/18S amplicon sequences using tools such as qiime2, DADA2, deblur, and bbtools
      Shell
      •
      GNU General Public License v3.0
      •11•0•0•0•Updated Nov 26, 2025Nov 26, 2025

    • snakemake-profiles

      Public
      0•0•0•0•Updated Jun 6, 2025Jun 6, 2025

    • Metagenome-Workflow

      Public
      branch currently used for bee bread samples WITHOUT host DNA removal
      Nextflow
      •
      MIT License
      •0•1•1•0•Updated Mar 24, 2025Mar 24, 2025

    • BRAKER

      Public
      BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
      Perl
      •
      Other
      •90•0•0•0•Updated Jan 22, 2025Jan 22, 2025

    • screfmapping

      Public
      R
      •
      Other
      •3•0•0•0•Updated Jan 10, 2025Jan 10, 2025

    • workflows-nextflow-2023

      Public
      Workflow management with Nextflow and nf-core
      HTML
      •
      Other
      •40•0•0•0•Updated Dec 4, 2024Dec 4, 2024

    • figaro

      Public
      An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters
      Python
      •
      GNU General Public License v3.0
      •26•0•0•0•Updated Oct 25, 2024Oct 25, 2024

    • 515F-Y_926R_database_construction

      Public
      A repository containing code for constructing qiime2 databases for the "Parada primers" (515F-Y / 926R). See linked OSF repo for the actual artifacts for specif…
      Shell
      •3•0•0•0•Updated Jul 5, 2024Jul 5, 2024

    • Mayo-Genome-Assembly

      Public
      Perl
      •0•0•2•0•Updated Jun 26, 2024Jun 26, 2024

    • Li_scATACSeq_demultiplexing_Nov23

      Public
      Shell
      •0•0•0•0•Updated Jun 10, 2024Jun 10, 2024

    • hergenrother-16S-mouse-2022Sept

      Public
      Code for the Hergenrother 2022 mouse antimicrobial study
      R
      •1•1•1•0•Updated Apr 19, 2024Apr 19, 2024

    • Refgraph_pipeline

      Public
      H3ABioNet RefGraph assembly-based pipeline
      Shell
      •6•0•0•0•Updated Feb 26, 2024Feb 26, 2024

    • dotPlotly

      Public
      Generate an interactive dot plot from mummer or minimap alignments
      HTML
      •
      MIT License
      •60•0•0•0•Updated Jan 17, 2024Jan 17, 2024

    • caceres-16S-mosquito-2022Sept

      Public
      R
      •0•1•0•0•Updated Nov 8, 2023Nov 8, 2023

    • bishop-Shoreline-Dec2021

      Public
      0•0•0•0•Updated Oct 23, 2023Oct 23, 2023

    • spams-R

      Public
      R interface for SPAMS (SPArse Modeling Software)
      C++
      •
      GNU General Public License v3.0
      •3•0•0•0•Updated Oct 12, 2023Oct 12, 2023

    • reference_database_creator

      Public
      creating reference databases for amplicon sequencing
      Python
      •
      MIT License
      •12•0•0•0•Updated Sep 29, 2023Sep 29, 2023

    • nextflow-training

      Public
      Nextflow training material
      Nextflow
      •
      Other
      •268•0•0•0•Updated Jul 31, 2023Jul 31, 2023

    • Pangenome-Graphs-Workshop

      Public
      This repository contains material to construct pangenome graphs for a small bacteria dataset detailing every step in the Nesi environment.
      HTML
      •
      GNU General Public License v2.0
      •3•0•0•0•Updated Jul 26, 2023Jul 26, 2023

    • smrnaseq

      Public
      A small-RNA sequencing analysis pipeline
      Nextflow
      •
      MIT License
      •133•0•0•0•Updated Jun 6, 2023Jun 6, 2023

    • dot

      Public
      Dot: An interactive dot plot viewer for comparative genomics
      JavaScript
      •
      MIT License
      •21•0•0•0•Updated May 4, 2023May 4, 2023

    • Detect-seq

      Public
      An unbiased method for genome-wide CBE off-targets assessment
      Python
      •
      Other
      •10•0•0•0•Updated Feb 22, 2023Feb 22, 2023

    • EM-seq

      Public
      Tools and Data related to Enzymatic Methylation Sequencing
      Nextflow
      •
      GNU Affero General Public License v3.0
      •8•0•0•0•Updated Jan 25, 2023Jan 25, 2023

    • TRIDENT

      Public
      NGS variant analysis & fluctuation analysis MLE calculator
      Jupyter Notebook
      •1•0•0•0•Updated Sep 12, 2022Sep 12, 2022

    • eib-marker-design

      Public
      Workflow for designing KASP markers from resequencing data
      R
      •
      MIT License
      •2•3•0•0•Updated Aug 12, 2022Aug 12, 2022