spearfish Paper: Δ-Mapping Speeds Up Long-Read Alignment to Redundant Transcriptomes

anshulkundaje · x · 2026-11-08

• Rob Patro's group (U. Maryland) and collaborators released spearfish on bioRxiv: an ultrafast long-read mapper built for redundant transcriptomes, where isoforms share most sequence and gene families add near-copies.
• Core idea: Δ-mapping computes each target's alignment-score difference from the best candidate; sequence shared by all candidates is skipped since it can't change the difference, and divergent regions are aligned once per distinct sequence instead of once per isoform.
• Seeds come from locally consistent parsing (LCP); collapsing them yields a de Bruijn-like core graph bounded by distinct exonic sequence plus a small per-splice-junction term. Code is available.

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