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

We present here FrangiPANe (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.