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use_case_examples/use-case-examples.md

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 # Biological Application
 
+Does YACHT provide qunatitative data?
+How sensitive is Yacht in detecting viruses?
+Could we use YACHT to identify the amount of host DNA?
+Is sequencing depth an issue for YACHT?
+Can YACHT be used to identify the amount of contamination that there is in a sample?
+
 ## Contamination Detection
 
 Identifying contamination of samples is an important step for downstream analysis. 
@@ -39,5 +45,9 @@ Early and accurate pathogen detection is vital for rapid diagnostic and clinical
 
 Research in pathogen detection have led to improvements of the experimental part such as differential lysis of human cells, etc. Further, efforts in improving computational tools and pipelines for pathogen detection have also been made such as real time pathogen detection (EPI2ME, SURPI-RT, etc)
 
+Methods for pathogen detection include PCR, multiplex PCR, broad-range PCR, antigen detection, MALDI-TOF MS, and PNA-FISH. However, PCR based methods are limited to false negatives, knowledge priori, and/or viral detection. Further, antigen detection is limited to the time for antibodies to develop which can take 1-2 weeks. Finally, methods such as mass spectrometry and insitu hybridization have been advancements for bacterial and fungal identification but still require bacterial cltivation, do not provide quantitative results (in the case of MALDI-TOF MS) or are limited to tissue samples (in the case of PNA-FISH). 
+
+Using clinical metagenomic data, we can detect any pathogenic infection (i.e. respiratory, bloodstream, central nervous system infections) without prior knowledge from millions of reads produced by shot gun metagenomic sequencing. 
+
 ### Pathogenic Detection Examples