The Nicotiana benthamiana genome data:
 \annotation
   directory with the gene model annotation files. 
 \assembly
   directory with the genome assembly files
 \repeats
   directory with the repeats dataset.

Currently there are three genome assembly versions
and one genome annotation.

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About genome assembly:
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 Niben.v0.3, assembly made by with 1 Illumina HiSeq2000 run: 
   5 lanes of PE-500bp, 
   1 lane of MP-2Kb and 
   1 lane of MP-5Kb, 
   using ABySS as assembler (Kmer 63).
 Niben.v0.4.3, same assembly that v0.3 using SOAPdenovo as 
   assembler, and the SOAP scripts to correct the reads and
   to fill the gaps. 
 Niben.v0.4.4, same assembly that v0.4.3 with the chloroplast
   sequence filtering.

 For more information: 
  Bombarely A. et al. 2012
  A draft genome sequence of Nicotiana benthamiana to enhance
  molecular plant-microbe biology research
  (Accepted for publication)
  http://dx.doi.org/10.1094/MPMI-06-12-0148-TA

About sequence IDs and assembly files. There are two assembly
files per version.

 Niben.genome.vX.X.scaffolds.nrcontigs.fasta, 
  with the scaffolds and the contigs that are not included in 
  the scaffolds (nrcontigs).
 Niben.genome.vX.X.contigs.fasta, 
  with all the contigs.

 ID for scaffolds: NibenXXXScfYYYYYYYY where XXX is the 
  assembly version and YYYYYYYY is the scaffold number.
 ID for nrcontigs: NibenXXXCtgYYYYYYYY where XXX is the
  assembly version and YYYYYYYY is the contig number.
 ID for contigs from scaffolds: NibenXXXScfYYYYYYYYCtgZZZ
  where XXX is the assembly version, YYYYYYYY is the 
  scaffold number and ZZZ is the contig number starting
  for the scaffold 5-prime.

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About the genome annotation:
============================================================ 
 
The current version was performed over the assembly version 
Niben.v0.4.4 (scaffolds and nrcontigs) using Maker 
(Cantarel B. et al. 2008) and RNAseq data supplied by 
Prof. Gregory Martin.

 ID for Gene models: NbXYYYYYYYYgZZZZ where X is 'S' for 
 scaffolds and 'C' for nrcontigs, YYYYYYYY is the number of
 the scaffold or the contig and ZZZZ is the number of the
 gene starting for the 5-prime of the scaffold or nrcontig
 sequence.

See README file in the annotation folder for more 
information

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 For any question, please contact with Prof. Gregory Martin
 (gbm7@cornell.edu)


                                 Ithaca, NY, Oct. 17th. 2012