Embl file description

The embl file shows the type of the patch. Type 1 are sequence differences between the current P. falciparum 3D7 assembly version 3.1 and a new P. falciparum 3D7 PacBio assembly. Around 500 bp are provided on each side as anchor. Type 2 are new genes, that are either anchored on both sides (type 2.1), or not anchored (type 2.2). Type 3 are dimorphic genes that are either anchored on both sides (type 3.1) or anchored on one side (type 3.2). Also in the embl is the chromosome, the coordinates of the patch on P. falciparum version 3.1 and the lab strain (P. falciparum IT, P. falciparum DD2 and P. falciparum HB3) the patch was taken from. To create Pfref1, embl files need to be aligned to P. falciparum 3D7 v3.1. Type 2.2 cannot be aligned. This needs to be analysed separately.