These two genomes are assemblies used in 
https://wellcomeopenresearch.org/articles/3-52/v1

Pf3D7PbUN.fasta is the raw output without ICORN2 correction.
Pf3D7_II.Jun2015.fasta is the PacBio assembly after our correction steps.

There genomes were not annotated. If needed, we suggest to use companion - http://companion.gla.ac.uk/. Use at RATT parameter "Assembly".