scAN1.0: A reproducible and standardized pipeline for processing 10X single cell RNAseq data

Area of Science:

• Computational Biology
• Genomics
• Bioinformatics

Background:

• Single cell transcriptomics is rapidly advancing, necessitating robust data analysis solutions.
• Existing pipelines often lack reproducibility, modularity, and interoperability.
• There is a growing demand for standardized and adaptable single-cell RNA sequencing (scRNA-seq) analysis tools.

Purpose of the Study:

• To introduce scAN1.0, a novel processing pipeline for 10X single-cell RNA sequencing data.
• To provide a reproducible, modular, and interoperable solution for scRNA-seq data analysis.
• To demonstrate the pipeline's utility in evaluating specific analysis steps, such as data mapping.

Main Methods:

• Development of scAN1.0 using the Nextflow Domain Specific Language 2 (DSL2).
• Implementation of a modular pipeline design for flexible integration of analysis modules.
• Application of scAN1.0 to two distinct scRNA-seq datasets: human pituitary tumor and murine CD8 T cells.

Main Results:

• scAN1.0 is demonstrated to be executable on diverse computational systems.
• The pipeline's modularity facilitates the evaluation of different analysis components.
• The study showcases scAN1.0's capability to assess the impact of the mapping step in scRNA-seq analysis.

Conclusions:

• scAN1.0 offers a versatile and reliable platform for analyzing 10X single-cell RNA sequencing data.
• The pipeline addresses the need for reproducible and interoperable computational tools in transcriptomics.
• scAN1.0 supports in-depth examination of analysis steps, contributing to more robust biological insights.