Predict Module

The predict module provides functions for predicting genes in genome assemblies.

Key Functions

predict

This is the main function for predicting genes in genome assemblies. It takes a genome FASTA file as input and produces a GFF3 file with gene predictions as output.

check_inputs

Checks that the input files exist and are valid.

run_genemark_es

Runs GeneMark-ES on the genome assembly.

run_augustus

Runs Augustus on the genome assembly.

run_miniprot

Runs Miniprot to align protein evidence to the genome assembly.

run_minimap2_transcripts

Runs Minimap2 to align transcript evidence to the genome assembly.

run_minimap2_proteins

Runs Minimap2 to align protein evidence to the genome assembly.

merge_predictions

Merges gene predictions from multiple sources.