PerSeqPIPE: Nextflow workflow for per-sequence analysis of small RNA-sequencing data

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ID: 331746
2026
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Abstract
Abstract Summary Small RNA sequencing enables high-throughput profiling of diverse small non-coding RNAs, but their complex biology creates substantial bioinformatic challenges. Conventional gene-centric pipelines often discard multi-mapping reads or impose arbitrary feature assignments, leading to biased quantification results. We present PerSeqPIPE, a modular, fully containerized Nextflow pipeline implementing a sequence-centric approach that quantifies each unique read sequence and annotates it with all compatible genomic and transcriptomic features. This preserves biologically relevant signals and enables broad small non-coding RNA profiling. PerSeqPIPE integrates harmonized reference resources for multiple small non-coding RNA classes and supports reproducible execution using Docker and Apptainer. The accompanying Streamlit-based PerSeqPIPE VIZ application enables interactive exploration, filtering, visualization, and differential expression analysis. Application to a published extracellular vesicle dataset revealed isomiR diversity and multi-mapped sncRNAs that were obscured by conventional approaches. Together, PerSeqPIPE and PerSeqPIPE VIZ provide an open, scalable, and transparent framework for small RNA-seq analysis. Availability and implementation PerSeqPIPE is freely available at https://github.com/ktrachtova/perseqpipe and PerSeqPIPE VIZ at https://github.com/ktrachtova/perseqpipe_viz. PerSeqPIPE is implemented in Nextflow, Python, Bash, and R; PerSeqPIPE VIZ is a Streamlit app. Both are compatible with macOS and Linux operating systems.
Reference Key
openalex_W7220846218 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Karolína Trachtová, Dagmar Al Tukmachi, Vojtěch Bystrý, Ondřej Slabý
Journal Bioinformatics advances
Year 2026
DOI
10.1093/bioadv/vbag294
URL
https://doi.org/10.1093/bioadv/vbag294
Keywords Keywords not found

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