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    13 repositories

    • ngs-academy

      Public
      JavaScript
      •1•1•2•0•Updated Aug 28, 2026Aug 28, 2026

    • proteomics-pipelines

      Public
      A repo with a proteogenomics and metaproteomics pipeline developed by Matthys Potgieter.
      Jupyter Notebook
      •
      MIT License
      •4•9•0•7•Updated Dec 31, 2024Dec 31, 2024

    • bacterial_variant_calling

      Public
      A pipeline for variant calling on bacterial genomes created with Nextflow and singularity / docker
      Nextflow
      •
      MIT License
      •5•1•2•1•Updated Jul 24, 2023Jul 24, 2023

    • bst-sysadmin

      Public
      Scripts for maintaining services and setup on the bst.cbio.uct.ac.za server. Also contain some scripts to pull info from the BST Redmine instance.
      Shell
      •
      MIT License
      •0•0•0•0•Updated Jul 5, 2021Jul 5, 2021

    • software-demo

      Public
      Testing github for hosting releases of in-house software
      HTML
      •
      MIT License
      •0•0•0•0•Updated Dec 22, 2020Dec 22, 2020

    • RNAseq-pipeline

      Public
      RNA sequencing analysis pipeline using STAR or HISAT2, with gene counts and quality control
      Nextflow
      •
      MIT License
      •892•0•0•0•Updated Feb 12, 2020Feb 12, 2020

    • 16S-rDNA-pipeline

      Public
      This repository contains an older version of our 16S rDNA diversity analysis pipeline. It uses a combination of bash scripts. To get a more updated version of t…
      R
      •
      MIT License
      •3•2•0•0•Updated Nov 27, 2019Nov 27, 2019

    • varscan

      Public
      Variant calling and somatic mutation/CNV detection for next-generation sequencing data
      34•0•0•0•Updated Jul 25, 2019Jul 25, 2019

    • 16S-rDNA-dada2-pipeline

      Public
      dada2 Nextflow pipeline
      Nextflow
      •
      MIT License
      •20•2•0•0•Updated May 31, 2019May 31, 2019

    • uct-srst2

      Public
      MLST using srst2, implemented in Nextflow
      Nextflow
      •
      GNU General Public License v3.0
      •3•0•0•0•Updated May 22, 2019May 22, 2019

    • 16S-rDNA-decon-pipeline

      Public
      Decontamination module
      Shell
      •
      MIT License
      •1•0•0•0•Updated Oct 20, 2018Oct 20, 2018

    • galaxy-tools

      Public
      This repos contain Galaxy tools and setup code of the UCT CBIO Galaxy server. It mainly contained customised tools for EST annotation and mapping of expression …
      Perl
      •
      MIT License
      •0•0•0•0•Updated Mar 22, 2018Mar 22, 2018

    • strep-wgs-pbp-pipeline

      Public
      Strep pneumoniae whole genome sequencing pipeline. The code in this repos was developed by Katie. It was done for a special request from the Medical Microbiolog…
      Shell
      •
      MIT License
      •1•0•0•0•Updated Mar 6, 2018Mar 6, 2018
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