Supporting data and code for the African Rice Panreference produced by the frangiPANe software

  • Christine Tranchant (Creator)
  • Clothilde Chenal (Creator)
  • Mathieu Blaison (Creator)
  • Laurence Albar (Creator)
  • Valentin Klein (Creator)
  • C├ędric Mariac (Creator)
  • Rod Wing (Creator)
  • Yves Vigouroux (Creator)
  • Francois Sabot (Creator)
  • Christine Tranchant (Contributor)

Dataset

Description

We present here FrangiPANe (https://github.com/tranchant/frangiPANe), a pipeline developed to build panreference using short reads through a map-then-assemble strategy and a dataset corresponding to 515 Mb of new sequences (484,394 non redundant sequences) in addition to the CG14 genome (iOMAP consortium). Applying this approach to 248 African rice genomes, we identified an average of 8 Mb of new sequences and 5,290 new contigs per individual. In total, 1.4 G of new sequences, consisting of 1,306,676 contigs, were assembled. FrangiPANe also allowed the anchoring of 31.5% of the new contigs within the CG14 reference genome, with a 92.5% accuracy at 2kb span. We annotated in addition 3,252 new genes absent from the reference. The authors acknowledge the IRD i-Trop HPC (South Green Platform) from IRD Montpellier for providing resources that contributed to this work.
Date made available2022
PublisherDataSuds

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