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    18 repositories

    • miso-lims

      Public
      MISO: An open-source LIMS for NGS sequencing centres
      Java
      •
      GNU General Public License v3.0
      •125•0•0•0•Updated Apr 14, 2026Apr 14, 2026

    • reform

      Public
      Modify existing reference fasta and gff3/gtf files to include a new sequence
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •6•33•5•1•Updated Feb 27, 2026Feb 27, 2026

    • GENEFLOW

      Public
      Genomic Examination and Nucleotide Evaluation For Laboratory Operations Workflow
      Python
      •1•0•10•6•Updated Dec 17, 2025Dec 17, 2025

    • variant-calling-pipeline-lr

      Public
      A comprehensive Nextflow pipeline for long-read variant calling and structural variant detection from Oxford Nanopore and PacBio sequencing data
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Dec 10, 2025Dec 10, 2025

    • reformWeb

      Public
      Flask WebUI for reform
      Python
      •2•0•0•4•Updated Jul 1, 2025Jul 1, 2025

    • hpc-gatk4

      Public
      Nextflow
      •0•0•1•0•Updated Jul 13, 2023Jul 13, 2023

    • variant-calling-pipeline-gatk4

      Public
      Variant Calling Pipeline Using GATK4 and Nextflow
      bioinformaticsgenomicsnextflow
      bioinformaticsgenomicsnextflowbioinformatics-pipelinevariant-callinggatk4
      Nextflow
      •49•59•1•1•Updated Feb 16, 2023Feb 16, 2023

    • MAD2

      Public
      Python
      •0•0•0•0•Updated Jul 27, 2022Jul 27, 2022

    • django-shibboleth-remoteuser

      Public
      Middleware for using Shibboleth with Django
      Python
      •
      MIT License
      •75•0•0•0•Updated Jun 28, 2022Jun 28, 2022

    • MAD

      Public
      Minor Allele Detection Pipeline for SARS-CoV2
      bioinformaticsgenomicsngs
      bioinformaticsgenomicsngscovid-19sars-cov-2sars-cov-2-variants
      Python
      •1•1•0•0•Updated Jul 15, 2021Jul 15, 2021

    • covid19

      Public
      Variant Analysis Pipeline for COVID19
      Nextflow
      •1•4•0•0•Updated Apr 30, 2021Apr 30, 2021

    • ReSeq

      Public
      More realistic simulator for genomic DNA sequences from Illumina machines that achieves a similar k-mer spectrum as the original
      C++
      •
      MIT License
      •3•0•0•0•Updated Feb 13, 2021Feb 13, 2021

    • mpileupplugin

      Public
      A JBrowse plugin for plotting allele fraction data
      JavaScript
      •1•0•0•0•Updated Jun 19, 2020Jun 19, 2020

    • variant-calling-pipeline

      Public
      HPC based pipelines for variant calling using GATK
      Shell
      •23•17•0•0•Updated Apr 6, 2020Apr 6, 2020

    • nf-workflows

      Public
      Repository of NextFlow Workflows
      Nextflow
      •0•4•0•0•Updated Mar 26, 2020Mar 26, 2020

    • r-notebooks

      Public
      Gene Set Enrichment Analysis and Over Representation Analysis analysis using R
      bioinformaticsgenomicsgsea
      bioinformaticsgenomicsgseaover-representation-analysisgene-set-enrichment-analysis
      24•21•3•0•Updated Jun 20, 2019Jun 20, 2019

    • BADAS

      Public
      Collection of BADAS related resources
      Jupyter Notebook
      •0•1•0•0•Updated Oct 4, 2018Oct 4, 2018

    • utils

      Public
      0•0•0•0•Updated Apr 27, 2018Apr 27, 2018
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