Welcome to the QBiC analysis documentation!

This documentation contains the guidelines for running Bioinformatics analyses at QBiC. How to run nf-core pipelines, which are the latest tested releases and how to report the results.

You can contribute or add changes to the documentation, by making a pull request to the pipelines-docs github repository.

Additionally, this repository will collect background information for the different analysis types.

Analysis types

Pipeline releases

Pipeline releases that are currently used at QBiC.

WES & WGS analysis

WGS and WES sequencing

RNAseq analysis

RNA sequencing

16S amplicon sequencing

16S amplicon sequencing

HLA typing

HLA typing

scRNAseq analysis

Single-cell RNA sequencing

BCRseq / TCRseq analysis

BCR / TCR sequencing

guideseq analysis

Guideseq analysis

Clusters and remotes

markdown/running_jobs

Submitting jobs to the SLURM clusters

markdown/denbi_cloud

Setting up instances on deNBI denbi_cloud

markdown/igenomes

Updating igenomes resource on the cluster