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    13 repositories

    • ngs-academy

      Public
      JavaScript
      •1•1•0•0•Updated Jan 17, 2025Jan 17, 2025

    • 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
      •4•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
      •716•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 the pipeline using Nextflow please go here: https://github.com/h3abionet/h3abionet16S/tree/master/workflows-nxf
      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
      •19•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 data onto pathways. The code was last worked on in 2011.
      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 Microbiology lab. Gerrit just moved it over from the original BitBucket space.
      Shell
      •
      MIT License
      •1•0•0•0•Updated Mar 6, 2018Mar 6, 2018