ArticlebioRxiv : the preprint server for biology2026
Analysis of isoform complexity in pan-transcriptome graphs with atroplex.
Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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4 authors.
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Abstract
Motivation: Alternative splicing of precursor mRNA lets a single gene encode multiple isoforms by joining exons in different combinations. Long-read sequencing resolves this isoform diversity across tissues, cohorts, and conditions. However, the resulting pan-transcriptomes are structurally complex, and their analysis requires repeatedly searching the full catalogue, which is impractical without a queryable index. As splicing patterns differ across conditions, a structure is needed that captures the connectivity between exons, not just their coordinates, so isoforms can be compared by structure across cohorts. Results: We present atroplex, a framework that indexes pan-transcriptome annotations and transcript isoforms in a combined spatial index and graph overlay, capturing both exon coordinates and splice connectivity. atroplex classifies query transcripts against the index, tracks per-sample isoform presence, and enables crosscohort isoform comparison. We indexed 21,005 samples spanning multiple reference resources into a single queryable structure, yielding a comprehensive map of isoform complexity that supports improved transcript discovery and structural comparison across cohorts. Availability: atroplex is licensed under GPLv3 and available at https://github.com/ylab-hi/atroplex.
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