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GENOME DATA WEB ACCESS
Oak genome assembly PM1N

(haploid version: 12 pseudomolecules with 871 scaffolds + 538 unassigned scaffolds)

https://urgi.versailles.inra.fr/download/oak/Qrob_PM1N.fa.gz
Oak genome assembly V2_2N

(diploid version 2)

https://urgi.versailles.inra.fr/download/oak/Qrob_V2_2N.fa
Oak genome assembly V1_2N

(diploid version 1 from Plomion et al. 2016 Mol Ecol Res 16: 254-265) 

https://urgi.versailles.inra.fr/download/oak/Qrob_V1_2N.fa
Oak transcriptome

(de novo assembly)

https://urgi.versailles.inra.fr/download/oak/OCV4_assembly_final.fsa
Oak protein-coding sequences predicted on PM1N

(haploid version)

CDS (aa): https://urgi.versailles.inra.fr/download/oak/Qrob_PM1N_CDS_aa_20161004.fa

CDS (nt):  https://urgi.versailles.inra.fr/download/oak/Qrob_PM1N_CDS_nt_20161004.fa

GFF files
Gene prediction: https://urgi.versailles.inra.fr/download/oak/Qrob_PM1N_genes_20161004.gff.gz

 
  • 1,130 manual_v1 #genes predicted using mapping of gene from manual curation in assembly  v1
  • 47 manual_v2 #genes manually curated on the published version
  • 28,488 regular # [N<20%] AND [[length > 500 nt] OR [gene with length < 500 nt with oak transcript evidence > 90% of coverage]]
  • 515 uncomplete # [without start or/and stop] OR [N>20%]
  • 13,575 unreliable #”low confidence” genes with length < 500 nt without transcript evidence > 90% of coverage
Vcf files (somatic mutations and heterozygozity) Candidate_somatic_mutations.zip (README)

Heterozygous_sites_3P.zip (README)

 Intermediate genome assemblies Newbler_assembly_A3.fa.zip

Cabog_assembly_C2.fa.zip

Bash scripts (Estimation of heterozygosity of the reference genotype ā€œ3Pā€) scripts_3P.zip

 

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