{"record_type":"pith_number_record","schema_url":"https://pith.science/schemas/pith-number/v1.json","pith_number":"pith:2013:RYHINQLSDA6XRZ6EB3MKS5ENJW","short_pith_number":"pith:RYHINQLS","schema_version":"1.0","canonical_sha256":"8e0e86c172183d78e7c40ed8a9748d4d96f99485a9513c6556099378ab3f7bc5","source":{"kind":"arxiv","id":"1304.4766","version":1},"attestation_state":"computed","paper":{"title":"High-speed and accurate color-space short-read alignment with CUSHAW2","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.GN","authors_text":"Bernt Popp, Bertil Schmidt, Yongchao Liu","submitted_at":"2013-04-17T11:06:33Z","abstract_excerpt":"Summary: We present an extension of CUSHAW2 for fast and accurate alignments of SOLiD color-space short-reads. Our extension introduces a double-seeding approach to improve mapping sensitivity, by combining maximal exact match seeds and variable-length seeds derived from local alignments. We have compared the performance of CUSHAW2 to SHRiMP2 and BFAST by aligning both simulated and real color-space mate-paired reads to the human genome. The results show that CUSHAW2 achieves comparable or better alignment quality compared to SHRiMP2 and BFAST at an order-of-magnitude faster speed and signific"},"verification_status":{"content_addressed":true,"pith_receipt":true,"author_attested":false,"weak_author_claims":0,"strong_author_claims":0,"externally_anchored":false,"storage_verified":false,"citation_signatures":0,"replication_records":0,"graph_snapshot":true,"references_resolved":false,"formal_links_present":false},"canonical_record":{"source":{"id":"1304.4766","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.GN","submitted_at":"2013-04-17T11:06:33Z","cross_cats_sorted":[],"title_canon_sha256":"671683dab6d1e2ee3009304ee9a7592e1b208c528578af725301fd890285a1be","abstract_canon_sha256":"728a35556d28b565ddfb60a588bbe33cb60f87fb1068df71081293802400f4b3"},"schema_version":"1.0"},"receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T03:27:43.759972Z","signature_b64":"wwhb1DmsFepEW162Jb9Ms/tLW65zgSxbGZK9hpQu5xTYAuTCmq9+6pAXRXfL2otm+o9iyYkRjy+8pRbYSB3aAA==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"8e0e86c172183d78e7c40ed8a9748d4d96f99485a9513c6556099378ab3f7bc5","last_reissued_at":"2026-05-18T03:27:43.759259Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T03:27:43.759259Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"graph_snapshot":{"paper":{"title":"High-speed and accurate color-space short-read alignment with CUSHAW2","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.GN","authors_text":"Bernt Popp, Bertil Schmidt, Yongchao Liu","submitted_at":"2013-04-17T11:06:33Z","abstract_excerpt":"Summary: We present an extension of CUSHAW2 for fast and accurate alignments of SOLiD color-space short-reads. Our extension introduces a double-seeding approach to improve mapping sensitivity, by combining maximal exact match seeds and variable-length seeds derived from local alignments. We have compared the performance of CUSHAW2 to SHRiMP2 and BFAST by aligning both simulated and real color-space mate-paired reads to the human genome. The results show that CUSHAW2 achieves comparable or better alignment quality compared to SHRiMP2 and BFAST at an order-of-magnitude faster speed and signific"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1304.4766","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":""},"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"},"aliases":[{"alias_kind":"arxiv","alias_value":"1304.4766","created_at":"2026-05-18T03:27:43.759364+00:00"},{"alias_kind":"arxiv_version","alias_value":"1304.4766v1","created_at":"2026-05-18T03:27:43.759364+00:00"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1304.4766","created_at":"2026-05-18T03:27:43.759364+00:00"},{"alias_kind":"pith_short_12","alias_value":"RYHINQLSDA6X","created_at":"2026-05-18T12:27:59.945178+00:00"},{"alias_kind":"pith_short_16","alias_value":"RYHINQLSDA6XRZ6E","created_at":"2026-05-18T12:27:59.945178+00:00"},{"alias_kind":"pith_short_8","alias_value":"RYHINQLS","created_at":"2026-05-18T12:27:59.945178+00:00"}],"events":[],"event_summary":{},"paper_claims":[],"inbound_citations":{"count":0,"internal_anchor_count":0,"sample":[]},"formal_canon":{"evidence_count":0,"sample":[],"anchors":[]},"links":{"html":"https://pith.science/pith/RYHINQLSDA6XRZ6EB3MKS5ENJW","json":"https://pith.science/pith/RYHINQLSDA6XRZ6EB3MKS5ENJW.json","graph_json":"https://pith.science/api/pith-number/RYHINQLSDA6XRZ6EB3MKS5ENJW/graph.json","events_json":"https://pith.science/api/pith-number/RYHINQLSDA6XRZ6EB3MKS5ENJW/events.json","paper":"https://pith.science/paper/RYHINQLS"},"agent_actions":{"view_html":"https://pith.science/pith/RYHINQLSDA6XRZ6EB3MKS5ENJW","download_json":"https://pith.science/pith/RYHINQLSDA6XRZ6EB3MKS5ENJW.json","view_paper":"https://pith.science/paper/RYHINQLS","resolve_alias":"https://pith.science/api/pith-number/resolve?arxiv=1304.4766&json=true","fetch_graph":"https://pith.science/api/pith-number/RYHINQLSDA6XRZ6EB3MKS5ENJW/graph.json","fetch_events":"https://pith.science/api/pith-number/RYHINQLSDA6XRZ6EB3MKS5ENJW/events.json","actions":{"anchor_timestamp":"https://pith.science/pith/RYHINQLSDA6XRZ6EB3MKS5ENJW/action/timestamp_anchor","attest_storage":"https://pith.science/pith/RYHINQLSDA6XRZ6EB3MKS5ENJW/action/storage_attestation","attest_author":"https://pith.science/pith/RYHINQLSDA6XRZ6EB3MKS5ENJW/action/author_attestation","sign_citation":"https://pith.science/pith/RYHINQLSDA6XRZ6EB3MKS5ENJW/action/citation_signature","submit_replication":"https://pith.science/pith/RYHINQLSDA6XRZ6EB3MKS5ENJW/action/replication_record"}},"created_at":"2026-05-18T03:27:43.759364+00:00","updated_at":"2026-05-18T03:27:43.759364+00:00"}