{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2017:UXV3ZEJNUMM3IWV22DH3MVLDQC","short_pith_number":"pith:UXV3ZEJN","canonical_record":{"source":{"id":"1703.09852","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.GN","submitted_at":"2017-03-29T00:58:02Z","cross_cats_sorted":[],"title_canon_sha256":"beb0c0bd55421a8b3cdc34cc282ef49827bdba63ffe3f3bb1c3fa36818f5b7fa","abstract_canon_sha256":"d91deaa99be6026d19c9d1a89478f66722d4e68d97936437088b560fe31c1ca9"},"schema_version":"1.0"},"canonical_sha256":"a5ebbc912da319b45abad0cfb6556380a182b1a5174b7017c4ede732a38831b0","source":{"kind":"arxiv","id":"1703.09852","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1703.09852","created_at":"2026-05-18T00:47:39Z"},{"alias_kind":"arxiv_version","alias_value":"1703.09852v1","created_at":"2026-05-18T00:47:39Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1703.09852","created_at":"2026-05-18T00:47:39Z"},{"alias_kind":"pith_short_12","alias_value":"UXV3ZEJNUMM3","created_at":"2026-05-18T12:31:49Z"},{"alias_kind":"pith_short_16","alias_value":"UXV3ZEJNUMM3IWV2","created_at":"2026-05-18T12:31:49Z"},{"alias_kind":"pith_short_8","alias_value":"UXV3ZEJN","created_at":"2026-05-18T12:31:49Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2017:UXV3ZEJNUMM3IWV22DH3MVLDQC","target":"record","payload":{"canonical_record":{"source":{"id":"1703.09852","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.GN","submitted_at":"2017-03-29T00:58:02Z","cross_cats_sorted":[],"title_canon_sha256":"beb0c0bd55421a8b3cdc34cc282ef49827bdba63ffe3f3bb1c3fa36818f5b7fa","abstract_canon_sha256":"d91deaa99be6026d19c9d1a89478f66722d4e68d97936437088b560fe31c1ca9"},"schema_version":"1.0"},"canonical_sha256":"a5ebbc912da319b45abad0cfb6556380a182b1a5174b7017c4ede732a38831b0","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T00:47:39.234485Z","signature_b64":"ik4BU55FUbNE0lD8Na46wenetL+ZWmCE3ydFG1FCBxbSXhuW1o28qQYYWqvR72KJaMaqVKYRgBsO7oc6thADCg==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"a5ebbc912da319b45abad0cfb6556380a182b1a5174b7017c4ede732a38831b0","last_reissued_at":"2026-05-18T00:47:39.233808Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T00:47:39.233808Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1703.09852","source_version":1,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-05-18T00:47:39Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"3bQTEs+3blN7v0V3SMCLG+Ev6TC4MCulRo0h+cwGZ8j0nJXjavOujqEaA/kamrL0vMnTrExezdWESkc2lwxfAg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-06-03T06:30:18.857895Z"},"content_sha256":"f5fd07f2e54037d897f998ef52b0298282b7c3227efec9e9b3cc09e593fa93c0","schema_version":"1.0","event_id":"sha256:f5fd07f2e54037d897f998ef52b0298282b7c3227efec9e9b3cc09e593fa93c0"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2017:UXV3ZEJNUMM3IWV22DH3MVLDQC","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Meraculous-2D: Haplotype-sensitive Assembly of Highly Heterozygous genomes","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.GN","authors_text":"Daniel Rokhsar, Eugene Goltsman, Isaac Ho","submitted_at":"2017-03-29T00:58:02Z","abstract_excerpt":"While many short read assemblers attempt to simplify the de Brujin graph by identifying and resolving variant-induced bubbles to produce a haploid mosaic result, this approach is only viable when variants are relatively rare and the bubbles are well defined in a graph context. We observed that diploid genomes with very high levels of heterozygosity fail to display well-resolved bubble structures in a typical assembly graph and thus result in highly fragmented and incomplete assemblies. Here we present an enhancement of Meraculous2 algorithm, called Meraculous-2D, which preserves haplotypes acr"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1703.09852","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"},"verdict_id":null},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-05-18T00:47:39Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"GVoKJN81mm0dyP7AEQ0gClo5gPG5haLDRq6bRovnasLc73lbu0brK2kkL5pjdAh/GfmY38NdZnMxaTNpVOoDBA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-06-03T06:30:18.858236Z"},"content_sha256":"605692afdaa22e0bf98b93a031588d65d45797f6c952ed3fb481ed898fb10d3e","schema_version":"1.0","event_id":"sha256:605692afdaa22e0bf98b93a031588d65d45797f6c952ed3fb481ed898fb10d3e"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/UXV3ZEJNUMM3IWV22DH3MVLDQC/bundle.json","state_url":"https://pith.science/pith/UXV3ZEJNUMM3IWV22DH3MVLDQC/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/UXV3ZEJNUMM3IWV22DH3MVLDQC/bundle.json","status":"primary"}],"public_keys":[{"key_id":"pith-v1-2026-05","algorithm":"ed25519","format":"raw","public_key_b64":"stVStoiQhXFxp4s2pdzPNoqVNBMojDU/fJ2db5S3CbM=","public_key_hex":"b2d552b68890857171a78b36a5dccf368a953413288c353f7c9d9d6f94b709b3","fingerprint_sha256_b32_first128bits":"RVFV5Z2OI2J3ZUO7ERDEBCYNKS","fingerprint_sha256_hex":"8d4b5ee74e4693bcd1df2446408b0d54","rotates_at":null,"url":"https://pith.science/pith-signing-key.json","notes":"Pith uses this Ed25519 key to sign canonical record SHA-256 digests. Verify with: ed25519_verify(public_key, message=canonical_sha256_bytes, signature=base64decode(signature_b64))."}],"merge_version":"pith-open-graph-merge-v1","built_at":"2026-06-03T06:30:18Z","links":{"resolver":"https://pith.science/pith/UXV3ZEJNUMM3IWV22DH3MVLDQC","bundle":"https://pith.science/pith/UXV3ZEJNUMM3IWV22DH3MVLDQC/bundle.json","state":"https://pith.science/pith/UXV3ZEJNUMM3IWV22DH3MVLDQC/state.json","well_known_bundle":"https://pith.science/.well-known/pith/UXV3ZEJNUMM3IWV22DH3MVLDQC/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2017:UXV3ZEJNUMM3IWV22DH3MVLDQC","merge_version":"pith-open-graph-merge-v1","event_count":2,"valid_event_count":2,"invalid_event_count":0,"equivocation_count":0,"current":{"canonical_record":{"metadata":{"abstract_canon_sha256":"d91deaa99be6026d19c9d1a89478f66722d4e68d97936437088b560fe31c1ca9","cross_cats_sorted":[],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.GN","submitted_at":"2017-03-29T00:58:02Z","title_canon_sha256":"beb0c0bd55421a8b3cdc34cc282ef49827bdba63ffe3f3bb1c3fa36818f5b7fa"},"schema_version":"1.0","source":{"id":"1703.09852","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1703.09852","created_at":"2026-05-18T00:47:39Z"},{"alias_kind":"arxiv_version","alias_value":"1703.09852v1","created_at":"2026-05-18T00:47:39Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1703.09852","created_at":"2026-05-18T00:47:39Z"},{"alias_kind":"pith_short_12","alias_value":"UXV3ZEJNUMM3","created_at":"2026-05-18T12:31:49Z"},{"alias_kind":"pith_short_16","alias_value":"UXV3ZEJNUMM3IWV2","created_at":"2026-05-18T12:31:49Z"},{"alias_kind":"pith_short_8","alias_value":"UXV3ZEJN","created_at":"2026-05-18T12:31:49Z"}],"graph_snapshots":[{"event_id":"sha256:605692afdaa22e0bf98b93a031588d65d45797f6c952ed3fb481ed898fb10d3e","target":"graph","created_at":"2026-05-18T00:47:39Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"graph_snapshot":{"author_claims":{"count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","strong_count":0},"builder_version":"pith-number-builder-2026-05-17-v1","claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"paper":{"abstract_excerpt":"While many short read assemblers attempt to simplify the de Brujin graph by identifying and resolving variant-induced bubbles to produce a haploid mosaic result, this approach is only viable when variants are relatively rare and the bubbles are well defined in a graph context. We observed that diploid genomes with very high levels of heterozygosity fail to display well-resolved bubble structures in a typical assembly graph and thus result in highly fragmented and incomplete assemblies. Here we present an enhancement of Meraculous2 algorithm, called Meraculous-2D, which preserves haplotypes acr","authors_text":"Daniel Rokhsar, Eugene Goltsman, Isaac Ho","cross_cats":[],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.GN","submitted_at":"2017-03-29T00:58:02Z","title":"Meraculous-2D: Haplotype-sensitive Assembly of Highly Heterozygous genomes"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1703.09852","kind":"arxiv","version":1},"verdict":{"created_at":null,"id":null,"model_set":{},"one_line_summary":"","pipeline_version":null,"pith_extraction_headline":"","strongest_claim":"","weakest_assumption":""}},"verdict_id":null}}],"author_attestations":[],"timestamp_anchors":[],"storage_attestations":[],"citation_signatures":[],"replication_records":[],"corrections":[],"mirror_hints":[],"record_created":{"event_id":"sha256:f5fd07f2e54037d897f998ef52b0298282b7c3227efec9e9b3cc09e593fa93c0","target":"record","created_at":"2026-05-18T00:47:39Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"attestation_state":"computed","canonical_record":{"metadata":{"abstract_canon_sha256":"d91deaa99be6026d19c9d1a89478f66722d4e68d97936437088b560fe31c1ca9","cross_cats_sorted":[],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.GN","submitted_at":"2017-03-29T00:58:02Z","title_canon_sha256":"beb0c0bd55421a8b3cdc34cc282ef49827bdba63ffe3f3bb1c3fa36818f5b7fa"},"schema_version":"1.0","source":{"id":"1703.09852","kind":"arxiv","version":1}},"canonical_sha256":"a5ebbc912da319b45abad0cfb6556380a182b1a5174b7017c4ede732a38831b0","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"a5ebbc912da319b45abad0cfb6556380a182b1a5174b7017c4ede732a38831b0","first_computed_at":"2026-05-18T00:47:39.233808Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T00:47:39.233808Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"ik4BU55FUbNE0lD8Na46wenetL+ZWmCE3ydFG1FCBxbSXhuW1o28qQYYWqvR72KJaMaqVKYRgBsO7oc6thADCg==","signature_status":"signed_v1","signed_at":"2026-05-18T00:47:39.234485Z","signed_message":"canonical_sha256_bytes"},"source_id":"1703.09852","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:f5fd07f2e54037d897f998ef52b0298282b7c3227efec9e9b3cc09e593fa93c0","sha256:605692afdaa22e0bf98b93a031588d65d45797f6c952ed3fb481ed898fb10d3e"],"state_sha256":"07489844972ad8db2a1f1712b565d2b8f346d9d424cbbd418982aa53a3dbedea"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"AR43YPsxdLwN510YhFCmF5uWUYvrbfMkS36eoExxCM2BXnjF9gt0Y/wT893mY/yo0Bk4hB5MWnjUDDWFJIUPCA==","signed_message":"bundle_sha256_bytes","signed_at":"2026-06-03T06:30:18.860160Z","bundle_sha256":"b41b96f8dbfaad5fde460304eaaefe27361033a25a24301ee07102710c8ac10c"}}