Introduction

nf-core/yascp is a bioinformatics best-practice analysis pipeline tailored for robuts donor deconvolutions, doublet detections, celltype assignemts, quality control, integration, clustering of single-cell datasets. YASCP enhances productivity by automating data preprocessing, quality control, and advanced analyses, ensuring high-quality results with minimal manual intervention. All you have to prepeare is a simple tsv file indicating the number of donors in pools and the path to cellrange folder:

experiment_id	n_pooled	donor_vcf_ids	data_path_10x_format
Pool1	1	""	path/to/cellranger/10x_folder
Pool2	2	""	path/to/cellranger/10x_folder

Results will demultiplex individuals, robustly assess the assignments

As well as assign celltypes, perform integrations, remove ambient RNA and produce publication ready plots

Developed under the leadership of N.Soranzo and Human Genetics Informatics (HGI), this large-scale single-cell pipeline was originally crafted for the Cardinal project (profiling UKBB and ELGH participants) but is versatile enough for broad scRNA analysis applications.

Input requires a tsv seperated file (please read detailed documentation here) with paths and if running in an genotype additional input is required to be provided in an input.nf file pointing to the vcf location. This pipeline is designed to be used any large scale single cell experiments.

The foundational ideas were inspired by earlier pipelines from Anderson lab but has been expanded, specifically those for deconvolution, cellbender, and quality control and clustering. This ensures a robust integration of proven methodologies tailored to meet the demands of expansive single-cell data analysis.

Quick Start

1. Install Nextflow (>=21.04.0)

2. Install any of Docker, Singularityfor full pipeline reproducibility.

3. Download/clone the pipeline and test it on a minimal dataset with a single command:

   git clone https://github.com/wtsi-hgi/yascp.git
   nextflow run /path/to/colned/yascp -profile test,<docker/singularity,institute>

Run on your own data

1. Prepeare input.tsv file:

experiment_id	n_pooled	donor_vcf_ids	data_path_10x_format
Pool1	1	""	path/to/cellranger/10x_folder
Pool2	2	""	path/to/cellranger/10x_folder

2. Run on your data

   git clone https://github.com/wtsi-hgi/yascp.git
   nextflow run /path/to/colned/yascp -profile test,<docker/singularity,institute> --input_data_table input.tsv

Pipeline summary

Pipeline has a modular design ensuring that the bits and piecies can be run independently according to project needs. Overall pipeline is focussed arounf main steps:

1. Cellbender
2. CellSNP
3. Vireo
4. Souporcell
5. Celltypist
6. Azimuth
7. BBKNN
8. Harmony
9. Scrublet, DoubletDecon, DoubletFinder, SCDS, scDblFinder, DoubletDetection
10. Sccaf
11. Lisi
12. Isolation Forest
13. Hard filters
14. Genotype deconvolution and GT match against multiple panels.
15. Citeseq DSB normalisations,
16. Cell genotype concordance Calculations

You can run pipeline blocks independently:

Documentation: Prepearing your own data and interpreting the results

To understand how to prepeare your own data and how to interpret the results please refear to documents HERE

Credits

Yascp was originally written by Matiss Ozols as part of the Cardinal project but is applicable to many other projects with contributions from Leland Taylor, Guillaume Noell, Hannes Ponstingl, Vivek Iyer, Henry Taylor, Tobi Alegbe, Monika Krzak, Alessandro Raveane, Carl Anderson, Anna Lorenc, Stephen Watt, Nicole Soranzo.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

Contributions and Support

We wellcome all contributions. If you would like to contribute to this pipeline, please create a fork and then create a pull request, and inform Matiss ([email protected]) re the changes made and additions added.

Citations

Currently pipeline has not been published but we would really appreciate if you could please acknowlage the use of this pipeline in your work:

Ozols, M. et al. 2023. YASCP (Yet Another Single Cell Pipeline): GitHub. https://github.com/wtsi-hgi/yascp.

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

We have used nf-cores template to develop this pipeline. You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines. Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.