use-case-example.md

use_case_examples/use-case-examples.md

@@ -9,28 +9,32 @@ Failure to detect sample contaminants can bias community diversity and strain sh
 There are two types of contaminants that yacht can detect. Specifically, external and cross contaminations. External contaminations includes any microbial DNA that can come from a researcher's native microbiome, experimental kits, and surrounding areas. Cross contamination can come from DNA extractions, sequencing index switching, and sample bleeding. Further, cross-contamination can complicate contimanation detection.
 
 Here, we explore how we can use YACHT for contaminant detection with the following tutorials:
-* External Contamination Detection Example
-* Cross Contamination Detection Example
-* Contamination in Low-biomass Datasets Example
+* External Contamination Detection 
+* Cross Contamination Detection 
+* Contamination in Low-biomass Datasets 
 
-### External Contamination Detection Example
+### Contaminant Detection Examples
+
+#### External Contamination Detection
 
 Data:
 
 Commands:
 
 Interpretation:
 
-### Cross Contamination Detection Example
+#### Cross Contamination Detection
 
 Data:
 
 Commands:
 
 Interpretation:
 
-### Contamination in Low-biomass Datasets Example
+#### Contamination in Low-biomass Datasets
 
 ## Pathogenic Detection
 
+Introduce...
 
+### Pathogenic Detection Examples