sRNAMap: a lightweight, browser-based web application for small RNA mapping, analysis and visualisation

Abstract

Small RNA (sRNA) sequencing is widely used to study siRNA, miRNA and piRNA pathways and to profile sRNAs derived from viruses, transposons and host transcripts. However, many sRNA workflows rely on command-line mapping and separate software for downstream analysis and visualisation. We present sRNAMap, an HTML5/JavaScript application for mapping and analysing sRNA sequencing data. sRNAMap accepts either raw FASTA/FASTQ reads or pre-aligned BAM files. For raw reads, sRNAMap uses a k-mer-seeded alignment algorithm that runs directly in the browser using parallel Web Workers where supported. It generates strand-specific per-base coverage, 5'- and 3';-end profiles, read-length distributions and nucleotide-bias summaries, with optional library-size normalisation. It also quantifies characteristic read-overlap signatures, including 5';-to-5'; overlaps associated with ping-pong-like processing. Additional modules quantify phased sRNA production, non-templated 3'- and 5'-additions, and sequence diversity. Analyses can be saved and restored as JSON or exported as self-contained HTML reports containing figures and analysis metadata. Benchmarking against Bowtie 2 under approximately matched alignment settings using a representative virus-infected arthropod small-RNA dataset showed highly concordant mapping profiles. Per-position depth showed an R^2 of approximately 0.998, while 5';- and 3';-end counts showed R^2 values of approximately 0.97. sRNAMap is available at https://github.com/rhparry/sRNAMap under the MIT licence.