Pinned Repositories
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
16SrRNA-hex-tutorial
16S rRNA marker gene upstream and dowstream analysis tutorial for the UCT Hex cluster.
batch-system-comp
Scripts showing some comparison between SLURM and PBS/TORQUE submissions
crypt4gh-tutorial
A tutorial on using Crypt4GH
HUPAN
Human pan-genome analysis pipeline
varcall
Nextflow scripts for doing variant calling on human samples
grbot's Repositories
grbot/16SrRNA-hex-tutorial
16S rRNA marker gene upstream and dowstream analysis tutorial for the UCT Hex cluster.
grbot/varcall
Nextflow scripts for doing variant calling on human samples
grbot/16s-int-bt
16S Intermediate Bioinformatics training manuals
grbot/16S-rDNA-dada2-pipeline
TADA - Targeted Amplicon Diversity Analysis - a DADA2-focused Nextflow workflow for any targeted amplicon region
grbot/HUPAN
Human pan-genome analysis pipeline
grbot/crypt4gh-tutorial
A tutorial on using Crypt4GH
grbot/containers
Repos with containers regularly used
grbot/azure-quickstart-templates
Azure Quickstart Templates
grbot/basic-submit
grbot/bioinftk
Some bioinformatics helper scripts
grbot/chip-2024-biosample
SQlite exercise
grbot/chip-2024-variant-calling
Variant calling workflow exercise
grbot/cram-qc
grbot/crypt4gh
GA4GH cryptographic tools
grbot/docker-action
grbot/elwazi-workshop-vm-setup
grbot/flagstat
grbot/ga4gh-starter-kit-drs
Open, extensible server implementation of the GA4GH Data Repository Service (DRS) specification
grbot/ga4gh-starter-kit-wes
Starter Kit server implementation of the GA4GH Workflow Execution Service (WES) specification
grbot/howfairis
Command line tool to analyze a GitHub or GitLab repository's compliance with the fair-software.eu recommendations
grbot/ilifu_user_docs
User documentation for the Ilifu project
grbot/multiqc
grbot/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
grbot/nf-rnaSeqCount
Assembly and differential expression analysis
grbot/pbbds-workshop-vm-setup
grbot/RpNRM
RpNRM
grbot/run-fastqc
Nextflow pipeline to test Singularity and SLURM for H3ABioNet GWAS workshop 2018
grbot/samtools-view-count-nf
Count the number of reads in a SAM/BAM/CRAM file using samtools view
grbot/sentieon-scripts
grbot/Tychus