Pipeline-description.md

@@ -463,7 +463,11 @@ braker.pl --genome=assembly.fasta --bam=file1.bam,file2.bam --prot_seq=prot1.fas
 
 **Version**: 1.4.4
 
-GeneID is tool used to predict genes in anonymous genomic sequences.
+GeneID is a tool used to predict genes in anonymous genomic sequences. It needs a parameter file that was generated during a training phase. Some parameter files are available for different organisme like *Vitis vinifera*. A tutoriel is available for training GeneID on a new organism, but it doesn't work properly. Based on the parameter file the prediction can be run on the assembly to annotate (the option *-3* is used to return the output in GFF3 format):
+
+```bash
+geneid assembly.fasta -P param_file -3 > output.gff3
+```
 
 ### Liftoff