Update README.md refining the subsampling and private data subsections

Author: DOH-LMT2303

README.md

@@ -18,7 +18,7 @@
 - [Repository File Structure Overview](#repository-file-structure-overview)
 - [Expected Outputs](#expected-outputs)
 - [Scientific Decisions](#scientific-decisions)
-- [Adapting for Another Jurisdiction](#adapting-for-another-jurisdiction)
+- [Customization for Local Adaptation](#customization-for-local-adaptation)
 - [Contributing](#contributing)
 - [License](#license)
 - [Acknowledgements](#acknowledgements)
@@ -109,9 +109,6 @@ _Mencattelli, G., Ndione, M.H.D., Silverj, A. et al. Spatial and temporal dynami
 The Washington focused WNV build uses the sequence [AF481864](https://www.ncbi.nlm.nih.gov/nuccore/AF481864) as this is the sequence that is most closely related to the sequences isolated from New York in 1999. 
 _Hadfield J, Brito AF, Swetnam DM, Vogels CBF, Tokarz RE, Andersen KG, Smith RC, Bedford T, Grubaugh ND. Twenty years of West Nile virus spread and evolution in the Americas visualized by Nextstrain. PLoS Pathog. 2019 Oct 31;15(10):e1008042. doi: 10.1371/journal.ppat.1008042. PMID: 31671157; PMCID: PMC6822705._
 
-### Subsampling
-The Washington focused WNV build pulls all the WNV sequences available in NCBI and filters the data in the phylogenetic workflow based on criteria defined in the config.yml file that is located inside the build-configs/washington-state folder. The subsampling criteria focuses on geographic location selecting all sequences from Washington, neighboring states, and region but up to a maximum of 5,000 sequences; and up to 300 sequences selected randomly from the rest of the states. All sequences have to meet a minimum genome length that is also specified as part of the subsampling criteria. There is more information about how to subsample data in Nextstrain here [Filter and Subsampling](https://docs.nextstrain.org/en/latest/guides/bioinformatics/filtering-and-subsampling.html)
-
 ### Lineage Designation
 For global lineage designations, we query [pathoplexus](https://pathoplexus.org/)
 
@@ -121,17 +118,16 @@ We further refined the information in the NCBI Host column by categorizing it in
 ### Determination of Minimum Genome Length
 The average genome length of WNV is 10,948 bp. Nextstrain's phylogenetic workflow defaults to excluding sequences with less than 90% genome coverage, as the alignment of short sequences can be unreliable. However, due to the limited number of WNV sequences available in NCBI, we evaluated minimum genome length thresholds of 90% (9,800 bp), 80% (8,700 bp), 75% (8,200 bp), and 70% (7,700 bp). For each threshold, we ran the Washington-focused build and compared: (1) the number of sequences included, (2) data gap locations in the alignment files using an alignment viewer, and (3) the topology and lineage assignments from the phylogenetic tree outputs to determine the optimal threshold. We concluded that a minimum genome length of 75% (8,200 bp) included a higher number of sequences while balancing alignment quality. Lastly, we validated this threshold using the global build.
 * To modify the minimum length of nucleotide sequence in the WNV global build enter the desired threshold in the --min-length <MIN_LENGTH> parameter that is listed in the [defaults/config.yaml](https://github.com/nextstrain/WNV/blob/main/phylogenetic/defaults/config.yaml) file
-* To modify the minimum length of nucleotide sequence in the WNV Washington focused build enter the desired threshold in the --min-length <MIN_LENGTH> parameter that is listed in the [washington-state/config.yaml](https://github.com/nextstrain/WNV/blob/main/phylogenetic/build-configs/washington-state/config.yaml) file
+* To modify the minimum length of nucleotide sequence in the WNV Washington focused build enter the desired threshold in the --min-length <MIN_LENGTH> parameter that is listed in the [washington-state/config.yaml](https://github.com/nextstrain/WNV/blob/main/phylogenetic/build-configs/washington-state/config.yaml) file.
 
-### Map Specific Locations
-We have added the option to map specific locations using coordinates. The sample data for this feature is available in the file `ingest/defaults/annotations.tsv`. this file is in long data format and contains information for six randomly selected places unrelated to WNV data. 
-This feature is useful for states or agencies that need to map the locations of mosquito traps, for example. If the data is sensitive, we recommend modifying the annotations.tsv file locally when running the build. 
-To visualize the locations in Auspice:
-1. Navigate to the **Map** options in the left panel.
-2. In the **Geographic resolution** dropdown menu, select the level of data you entered in the `annotations.tsv` file. For example, the sample data maps to location.
+## Customization for Local Adaptation
+This build can be customized for use by other jurisdictions, including as states, cities, counties, or countries.
+
+### Subsampling
+The Washington focused WNV build retrieves all available WNV sequences from NCBI and filters the data within the phylogenetic workflow based on criteria defined in the config.yaml file, located in the [build-configs/washington-state](https://github.com/nextstrain/WNV/blob/main/phylogenetic/build-configs/washington-state/config.yaml) folder. For details on the current subsampling configuration and instructions on modifying the criteria, refer to the [phylogenetic/build-configs/washington-state README.md](https://github.com/nextstrain/WNV/blob/main/phylogenetic/build-configs/washington-state/README.md).
 
-## Adapting for Another Jurisdiction
- *[Brief overview on how to adapt this build for another jurisdiction, such as a state, city, county, or country. Including links to Readmes in other sections that contain detailed instructions on what and how to modify the files]*
+### Incorporating Additional Metadata
+We have added the option to integrate additional metadata, which can include either public or sensitive information. This feature is especially useful for jurisdictions that need to annotate the phylogenetic trees or map visualizations in Auspice. For example, in the Washington focused WNV build, we mapped the centroids of zip codes where mosquito traps are located. This information is within the phylogenetic workflow in the metadata.tsv file, located in the [phylogenetic/data-private](https://github.com/nextstrain/WNV/tree/main/phylogenetic/data-private) folder. For more details on the current metadata configuration and instructions on modifying it, refer to the [phylogenetic/data-private README.md](https://github.com/nextstrain/WNV/tree/main/phylogenetic/data-private).
 
 ## Contributing
 For any questions please submit them to our [Discussions](insert link here) page otherwise software issues and requests can be logged as a Git [Issue](insert link here).