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@ARTICLE{Schmidt:838406,
      author       = {Schmidt, Maximilian HW and Vogel, Alexander and Denton,
                      Alisandra K and Istace, Benjamin and Wormit, Alexandra and
                      van de Geest, Henri and Bolger, Marie and Alseekh, Saleh and
                      Maß, Janina and Pfaff, Christian and Schurr, Ulrich and
                      Chetelat, Roger T. and Maumus, Florian and Aury, Jean-Marc
                      and Koren, Sergey and Fernie, Alisdair R. and Zamir, Daniel
                      and Bolger, Anthony and Usadel, Björn},
      title        = {{D}e novo {A}ssembly of a {N}ew {S}olanum pennellii
                      {A}ccession {U}sing {N}anopore {S}equencing},
      journal      = {The plant cell},
      volume       = {29},
      number       = {10},
      issn         = {1040-4651},
      address      = {Rockville, Md.},
      publisher    = {Soc.},
      reportid     = {FZJ-2017-07018},
      pages        = {2336-2348},
      year         = {2017},
      abstract     = {Updates in nanopore technology have made it possible to
                      obtain gigabases of sequence data. Prior to this, nanopore
                      sequencing technology was mainly used to analyze microbial
                      samples. Here, we describe the generation of a comprehensive
                      nanopore sequencing data set with a median read length of
                      11,979 bp for a self-compatible accession of the wild tomato
                      species Solanum pennellii. We describe the assembly of its
                      genome to a contig N50 of 2.5 MB. The assembly pipeline
                      comprised initial read correction with Canu and assembly
                      with SMARTdenovo. The resulting raw nanopore-based de novo
                      genome is structurally highly similar to that of the
                      reference S. pennellii LA716 accession but has a high error
                      rate and was rich in homopolymer deletions. After polishing
                      the assembly with Illumina reads, we obtained an error rate
                      of $<0.02\%$ when assessed versus the same Illumina data. We
                      obtained a gene completeness of $96.53\%,$ slightly
                      surpassing that of the reference S. pennellii. Taken
                      together, our data indicate that such long read sequencing
                      data can be used to affordably sequence and assemble
                      gigabase-sized plant genomes.},
      cin          = {IBG-2},
      ddc          = {570},
      cid          = {I:(DE-Juel1)IBG-2-20101118},
      pnm          = {582 - Plant Science (POF3-582) / 583 - Innovative
                      Synergisms (POF3-583)},
      pid          = {G:(DE-HGF)POF3-582 / G:(DE-HGF)POF3-583},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:29025960},
      UT           = {WOS:000414861100009},
      doi          = {10.1105/tpc.17.00521},
      url          = {https://juser.fz-juelich.de/record/838406},
}