Introducing bollito: a flexible pipeline for comprehensive single-cell RNA-seq analyses

We are proud to announce bollito, an automated, flexible and parallelizable computational pipeline for the comprehensive analysis of single-cell RNA-seq data.

Starting from FASTQ files or pre-processed expression matrices, bollito performs both basic and advanced tasks in single-cell analysis including quality control, read alignment, dimensionality reduction, clustering, cell-marker detection, differential expression, functional analysis, trajectory inference and RNA velocity. We have built bollito using the Snakemake workflow management system, which easily connects each execution step and facilitates the reproducibility of results.

Are you interested in bollito? We have published the tool in Bioinformatics, check it out here.  The pipeline, along with full documentation and tutorials is available here.