Gerrit Reinier Botha 's repositories
16SrRNA-hex-tutorial
16S rRNA marker gene upstream and dowstream analysis tutorial for the UCT Hex cluster.
16s-int-bt
16S Intermediate Bioinformatics training manuals
16S-rDNA-dada2-pipeline
TADA - Targeted Amplicon Diversity Analysis - a DADA2-focused Nextflow workflow for any targeted amplicon region
crypt4gh-tutorial
A tutorial on using Crypt4GH
containers
Repos with containers regularly used
azure-quickstart-templates
Azure Quickstart Templates
bioinftk
Some bioinformatics helper scripts
chip-2024-biosample
SQlite exercise
chip-2024-variant-calling
Variant calling workflow exercise
crypt4gh
GA4GH cryptographic tools
ga4gh-starter-kit-drs
Open, extensible server implementation of the GA4GH Data Repository Service (DRS) specification
ga4gh-starter-kit-wes
Starter Kit server implementation of the GA4GH Workflow Execution Service (WES) specification
howfairis
Command line tool to analyze a GitHub or GitLab repository's compliance with the fair-software.eu recommendations
ilifu_user_docs
User documentation for the Ilifu project
ncov2019-artic-nf
A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
nf-rnaSeqCount
Assembly and differential expression analysis
RpNRM
RpNRM
run-fastqc
Nextflow pipeline to test Singularity and SLURM for H3ABioNet GWAS workshop 2018
samtools-view-count-nf
Count the number of reads in a SAM/BAM/CRAM file using samtools view