Update 2.2.2_Viral_Taxonomy_and_Phylogeny_II.md

MGXlab · Sep 24, 2024 · 6d56dae · 6d56dae
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diff --git a/_episodes/2.2.2_Viral_Taxonomy_and_Phylogeny_II.md b/_episodes/2.2.2_Viral_Taxonomy_and_Phylogeny_II.md
@@ -186,7 +186,7 @@ One of the advantages of running geNomad is that it also outputs functional anno
 
 Now that we have results from many different tools and programs, we can build a table to compare and correlate them. You can build this table however you would like - using excel or python etc... If you are using python, I recommend using pandas [`df.merge`](https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.merge.html) or [`df.join`](https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.join.html) methods for this task. You will likely need to use it multiple times. Here's a sample of the type of table you need to build:
 
-| Contig   | Contig length (bp) | Coverage | Coverage | Coverage | Completeness | Contamination | Num Genes | Num Genes | Num Genes | Num Genes  | Num Genes  | Num Genes  | Num Genes | Num Genes | Num Genes | Taxonomy                                                        | Taxonomy                                                        | Host Prediction |
+| Contig   | Contig length (bp) | Coverage| Completeness | Contamination | Num Genes | Num Genes | Num Genes | Num Genes  | Num Genes  | Num Genes  | Num Genes | Num Genes | Num Genes | Taxonomy                                                        | Taxonomy                                                        | Host Prediction |
 | -------- | ------------------ | -------- | -------- | -------- | ------------ | ------------- | --------- | --------- | --------- | ---------- | ---------- | ---------- | --------- | --------- | --------- | --------------------------------------------------------------- | --------------------------------------------------------------- | --------------- |
 |          |                    | total      |              |               | CheckV    | CheckV    | CheckV    | Phannotate | Phannotate | Phannotate | GeNomad   | GeNomad   | GeNomad   | vConTACT3                                                       | GeNomad                                                         |                 |
 |          |                    |         |              |               | Total     | Viral     | Bacterial | Total      | Viral      | Bacterial  | Total     | Viral     | Bacterial |                                                                 |                                                                 |                 |