pipeline.md

What happens in this pipeline?

By running genome-annotation/main.nf you can generate a a selection of "hints" to guide a subsequent de novo annotation of the eukaryotic genome of your choice. The full pipeline processes data using the following steps for each data type:

Proteins:

• Exonerate

ESTs and transcriptome:

• Exonerate

RNA-seq reads:

• Fastp
• Hisat2
• Trinity
• Exonerate

Once a file with all possible extrinsic hints is generated, the following steps are run:

--augustus true:

• Augustus