discoSnp goes to RAD seq

We propose an adaptation of DiscoSnp for RadSeq data.

  • Novelties:
    • Clustering per locus
    • Predictions of variants close to sequence extremities
    • Order(s) of magnitude faster than Stack or IPyRAD.
  • Predictions have high precision (up to 99.3% on simulated data) with good recall (82.2% when using high precision parameters)
  • Applied on real biological data, RAD data from 259 specimens of Chiastocheta flies, morphologically assigned to 7 species, all individuals were successfully assigned to their species using both STRUCTURE and Maximum Likelihood phylogenetic reconstruction. Moreover, identified variants succeeded to reveal a within species structuration and the existence of two populations linked to their geographic distributions.



 

Pierre PETERLONGO

Permanent link to this article: https://team.inria.fr/genscale/discosnp-goes-to-rad-seq/