{"paper":{"title":"IndelFreeAligner: A Streaming Aligner for Comprehensive Gapless Alignment Against Terabase-Scale References","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.GN","authors_text":"Brian Bushnell","submitted_at":"2026-07-29T15:01:52Z","abstract_excerpt":"The comparison of short sequences to massive reference databases is a cornerstone of modern genomics, but it presents a significant scalability challenge. Traditional alignment tools rely on time- and memory-intensive pre-indexing of the reference, creating a substantial bottleneck for applications involving small query sets against terabase-scale data, such as CRISPR spacer analysis. Here we present IndelFreeAligner, a streaming, indel-free alignment tool that eliminates the preprocessing bottleneck. It operates in two modes: an indexed mode for larger query sets and a brute-force mode for ma"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2607.27291","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2607.27291/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}