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--- gene_prediction_just_augustus [2024/10/25 13:57] – created 134.190.144.194
+++ gene_prediction_just_augustus [2024/10/28 10:17] (current) – 134.190.221.230
@@ Line 1: / Line 1: @@
+====== Gene prediction with just Augustus ======
+By Jason Shao & Joran Martijn (Last Edited: October 28th 2024)
+====Intro====
+**Augustus** is an //ab initio// gene predictor that employs **H**idden **M**arkov **M**odels (HMMs) pre-trained on existing datasets. Training a custom HMM model with your own data is possible, but in this basic tutorial, we are only going to consider pre-existing models.
+====Example Usage====
+<code>
+source activate augustus-3.5.0
+# only required for species=generic
+export AUGUSTUS_CONFIG_PATH="/misc/scratch3/jasons/protist_gene_prediction/software/custom_augustus_config"
+augustus \
+    --species=generic \
+    <your genome> \
+    --gff3=on \
+    --outfile=<outfile name>.gff3
+conda deactivate
+</code>
+Note that the species here is set to generic to minimize biases for a divergent organism. If your organism is closely related to one of the pre-trained species below, you can specify that instead to yield a better prediction.
+If you decide to use a pre-trained species, then you don't have to include the export line. The reason for including the export line is because augustus had stopped shipping probability files with generic species around 3.3.3. Why have they done that, you might ask? Well, unfortunately it's another great mystery for which science cannot explain.
+====Pre-trained Species====
 ^ Identifier                       ^ Species                              ^ Major Lineage                ^
 | human                            | //Homo sapiens//                       | Opisthokonta (Metazoa)       |
@@ Line 7: / Line 33: @@
 | tribolium                        | //Tribolium castaneum//                | Opisthokonta (Metazoa)       |
 | schistosoma                      | //Schistosoma mansoni//                | Opisthokonta (Metazoa)       |
-| tetrahymena                      | //Tetrahymena thermophila//            | SAR (Alveolata)              |
+| **tetrahymena**                      | **//Tetrahymena thermophila//**            | **SAR (Alveolata)**             |
 | galdieria                        | //Galdieria sulphuraria//              | Archaeplastida (Plantae)     |
 | maize                            | //Zea mays//                           | Archaeplastida (Plantae)     |
-| toxoplasma                       | //Toxoplasma gondii//                  | SAR (Alveolata)              |
+| **toxoplasma**                       | **//Toxoplasma gondii//**                  | **SAR (Alveolata)**              |
 | caenorhabditis                   | //Caenorhabditis elegans//             | Opisthokonta (Metazoa)       |
 | aspergillus_fumigatus            | //Aspergillus fumigatus//              | Opisthokonta (Fungi)         |