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1. (WO2018039133) EXTENDING ASSEMBLY CONTIGS BY ANALZING LOCAL ASSEMBLY SUB-GRAPH TOPOLOGY AND CONNECTIONS
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Pub. No.: WO/2018/039133 International Application No.: PCT/US2017/047824
Publication Date: 01.03.2018 International Filing Date: 21.08.2017
IPC:
G06F 19/26 (2011.01) ,G06F 19/28 (2011.01)
G PHYSICS
06
COMPUTING; CALCULATING; COUNTING
F
ELECTRIC DIGITAL DATA PROCESSING
19
Digital computing or data processing equipment or methods, specially adapted for specific applications
10
Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
26
for data visualisation, e.g. graphics generation, display of maps or networks or other visual representations
G PHYSICS
06
COMPUTING; CALCULATING; COUNTING
F
ELECTRIC DIGITAL DATA PROCESSING
19
Digital computing or data processing equipment or methods, specially adapted for specific applications
10
Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
28
for programming tools or database systems, e.g. ontologies, heterogeneous data integration, data warehousing or computing architectures
Applicants:
PACIFIC BIOSCIENCES OF CALIFORNIA, INC. [US/US]; 1305 O'brien Drive Menlo Park, CA 94025, US
Inventors:
CHIN, Chen-shan; US
Agent:
SCHERER, David, C.; US
REAMEY, Robert, H.; US
ELROD-ERICKSON, Monicia; US
Priority Data:
62/378,57923.08.2016US
Title (EN) EXTENDING ASSEMBLY CONTIGS BY ANALZING LOCAL ASSEMBLY SUB-GRAPH TOPOLOGY AND CONNECTIONS
(FR) EXTENSION DE CONTIGS D'ENSEMBLE PAR ANALYSE DE TOPOLOGIE DE SOUS-GRAPHE D'ENSEMBLE LOCAL ET DE CONNEXIONS
Abstract:
(EN) Aspects of the present disclosure provide methods, systems, and computer program products for generating one or more extended contigs. Aspects of the exemplary embodiment include receiving input contigs for a genome; generating local assembly subgraphs including the ends of each contig; identifying subgraphs that unambiguously connect two contigs; and generating an extended contig in which the orientation and order of at least two contigs is determined. Extended contigs can include any number of linearly ordered and linked contigs.
(FR) Des aspects de la présente invention concernent des procédés, des systèmes et des produits de type programmes d'ordinateur pour générer un ou plusieurs contigs étendus. Des aspects de l'exemple de mode de réalisation consistent à recevoir des contigs d'entrée pour un génome; générer des sous-graphes d'ensemble local comprenant les extrémités de chaque contig; identifier des sous-graphes qui relient de manière non ambiguë deux contigs; et générer un contig étendu dans lequel l'orientation et l'ordre d'au moins deux contigs sont déterminés. Les contigs étendus peuvent comprendre un nombre quelconque de contigs ordonnés linéairement et reliés.
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Designated States: AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW
African Regional Intellectual Property Organization (ARIPO) (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW)
Eurasian Patent Office (AM, AZ, BY, KG, KZ, RU, TJ, TM)
European Patent Office (EPO) (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TR)
African Intellectual Property Organization (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG)
Publication Language: English (EN)
Filing Language: English (EN)