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. Author manuscript; available in PMC: 2020 Jan 1.
Published in final edited form as: Methods Mol Biol. 2019;1962:65–95. doi: 10.1007/978-1-4939-9173-0_5

Figure 5:

Figure 5:

The AUGUSTUS runs of the BRAKER pipeline that are above depicted like on the left as a single box, actually comprise two separate runs (right side) if both RNA-Seq and protein evidence is provided. First, evidence that occurs in both sources is filtered and weighted as reliable, i.e. manual hints for AUGUSTUS (green arrows). This reliable evidence is merged with the remaining RNA-Seq hints for a first AUGUSTUS run (red arrows). For another run, priority 5 is assigned to protein hints, and priority 4 is assigned to RNA-Seq hints (orange arrows), and both hints are merged with the reliable hints (blue arrows). These hints are used for a second AUGUSTUS run. The results of both runs are merged by the AUGUSTUS tool joingenes in a non-redundant fashion.