uct-cbio Goto Github PK

16s-rdna-dada2-pipeline

dada2 Nextflow pipeline

16s-rdna-decon-pipeline

Decontamination module

16s-rdna-pipeline

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

bacterial_variant_calling

A pipeline for variant calling on bacterial genomes created with Nextflow and singularity / docker

bst-sysadmin

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.

galaxy-tools

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.

ngs-academy

proteomics-pipelines

A repo with a proteogenomics and metaproteomics pipeline developed by Matthys Potgieter.

rnaseq-pipeline

RNA sequencing analysis pipeline using STAR or HISAT2, with gene counts and quality control

software-demo

Testing github for hosting releases of in-house software

strep-wgs-pbp-pipeline

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.

uct-srst2

MLST using srst2, implemented in Nextflow

varscan

Variant calling and somatic mutation/CNV detection for next-generation sequencing data