4 Assembly and scaffolding 3B-v116,136 scaff1,040 Mb3BACGTAGACTACA
5 Assembly and scaffolding 3B-v116,136 scaff1,040 MbCuration of the scaffoldingV. Barbe, S. Mangenot (Genoscope)18% Ns3B-v34,999 scaff992 Mb13% NsIntegration of BAC-end match positionsParsing of MP read positionsscaff00001scaff00013scaff00024scaff00008scaff00011scaff00007scaff00005
6 Assembly and scaffolding 3B-v116,136 scaff1,040 MbCuration of the scaffoldingV. Barbe, S. Mangenot (Genoscope)18% NsGap fillingSeq. error correctionsJM. Aury, A. Couloux (Genoscope)3B-v34,999 scaff992 Mb13% Ns3B-v4-8% NsIllumina readsWhole 3B Shotgun109,914 gaps filled126,290 bases corrected (error rate: 0.1%)
7 Assembly and scaffolding 3B-v116,136 scaffCuration of the scaffoldingV. Barbe, S. Mangenot (Genoscope)1,040 MbGap fillingSeq. error correctionsJM. Aury, A. Couloux (Genoscope)3B-v44,999 scaff992 MbRedundancy removal and scaffold mergingS. Theil (INRA GDEC)Pool_APool_Bctg1ctg22,808 scaff833 Mb3B-v443redundancy:160 MbscaffAssembler.pl
9 Ordering scaffolds SNP discovery 3B-v4432,808 scaff833 MbSNP discoverySureSelect® seq. capture (E. Paux, N. Cubizolles, E. Rey)BaitTEDNA captured from 10 genotypesgene52,265 baitsisbpProbeDesign.pl39,077 SNPs
10 Ordering scaffolds SNP discovery Genotyping mapping pop 3,075 SNPs Genetic mapping (P. Sourdille)Anchor map: 384 indiv Cs x Renan+ Neighbor map: 3865 markersLD mapping (F. Balfourier)367 lines from a core-collection
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