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    • miso-lims

      Public
      MISO: An open-source LIMS for NGS sequencing centres
      Java
      GNU General Public License v3.0
      125000Updated 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
      63351Updated Feb 27, 2026Feb 27, 2026
    • GENEFLOW

      Public
      Genomic Examination and Nucleotide Evaluation For Laboratory Operations Workflow
      Python
      10106Updated Dec 17, 2025Dec 17, 2025
    • A comprehensive Nextflow pipeline for long-read variant calling and structural variant detection from Oxford Nanopore and PacBio sequencing data
      Nextflow
      MIT License
      0000Updated Dec 10, 2025Dec 10, 2025
    • reformWeb

      Public
      Flask WebUI for reform
      Python
      2004Updated Jul 1, 2025Jul 1, 2025
    • hpc-gatk4

      Public
      Nextflow
      0010Updated Jul 13, 2023Jul 13, 2023
    • Variant Calling Pipeline Using GATK4 and Nextflow
      Nextflow
      495911Updated Feb 16, 2023Feb 16, 2023
    • MAD2

      Public
      Python
      0000Updated Jul 27, 2022Jul 27, 2022
    • Middleware for using Shibboleth with Django
      Python
      MIT License
      75000Updated Jun 28, 2022Jun 28, 2022
    • MAD

      Public
      Minor Allele Detection Pipeline for SARS-CoV2
      Python
      1100Updated Jul 15, 2021Jul 15, 2021
    • covid19

      Public
      Variant Analysis Pipeline for COVID19
      Nextflow
      1400Updated 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
      3000Updated Feb 13, 2021Feb 13, 2021
    • A JBrowse plugin for plotting allele fraction data
      JavaScript
      1000Updated Jun 19, 2020Jun 19, 2020
    • HPC based pipelines for variant calling using GATK
      Shell
      231700Updated Apr 6, 2020Apr 6, 2020
    • Repository of NextFlow Workflows
      Nextflow
      0400Updated Mar 26, 2020Mar 26, 2020
    • Gene Set Enrichment Analysis and Over Representation Analysis analysis using R
      242130Updated Jun 20, 2019Jun 20, 2019
    • BADAS

      Public
      Collection of BADAS related resources
      Jupyter Notebook
      0100Updated Oct 4, 2018Oct 4, 2018
    • utils

      Public
      0000Updated Apr 27, 2018Apr 27, 2018
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