miND (miRNA NGS Discovery pipeline): a small RNA-seq analysis pipeline and report generator for microRNA biomarker discovery studies [version 1; peer review: 2 approved with reservations]

• Published in: F1000 research Vol. 11; p. 233
• Main Authors: Diendorfer, Andreas, Khamina, Kseniya, Pultar, Marianne, Hackl, Matthias
• Format: Journal Article
• Language: English
• Published: 2022
• Subjects: discovery study; biomarkers; smallRNA sequencing; microRNA; differential expression; spike-in; Next-Generation Sequencing
• ISSN: 2046-1402; 2046-1402
• DOI: 10.12688/f1000research.94159.1

In contrast to traditional methods like real-time polymerase chain reaction, next-generation sequencing (NGS), and especially small RNA-seq, enables the untargeted investigation of the whole small RNAome, including microRNAs (miRNAs) but also a multitude of other RNA species. With the promising application of small RNAs as biofluid-based biomarkers, small RNA-seq is the method of choice for an initial discovery study. However, the presentation of specific quality aspects of small RNA-seq data varies significantly between laboratories and is lacking a common (minimal) standard. The miRNA NGS Discovery pipeline (miND) aims to bridge the gap between wet lab scientist and bioinformatics with an easy to setup configuration sheet and an automatically generated comprehensive report that contains all essential qualitative and quantitative results that should be reported. Besides the standard steps like preprocessing, mapping, visualization, and quantification of reads, the pipeline also incorporates differential expression analysis when given the appropriate information regarding sample groups. Although miND has a focus on miRNAs, other RNA species like tRNAs, piRNA, snRNA, or snoRNA are included and mapping statistics are available for further analysis. miND has been developed and tested on a multitude of data sets with various RNA sources (tissue, plasma, extracellular vesicles, urine, etc.) and different species. miND is a Snakemake based pipeline and thus incorporates all advantages using a flexible workflow management system. Reference databases are downloaded, prepared and built with an included (but separate) workflow and thus can easily be updated to the most recent version but also stored for reproducibility. In conclusion, the miND pipeline aims to streamline the bioinformatics processing of small RNA-seq data by standardizing the processing from raw data to a final, comprehensive and reproducible report.