nextstrain refine and metadata

nextstrain/README_NextStrain.md

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+# NextStrain Document
+
+## Installation
+
+### Install NextStrain into Conda env
+```
+curl http://data.nextstrain.org/nextstrain.yml --compressed -o nextstrain.yml
+conda env create --name nextstrain-env --file nextstrain.yml
+conda activate nextstrain-env
+npm install --global auspice
+```
+
+### Test the installation
+```
+conda activate nextstrain-env
+augur -h
+auspice -h
+nextstrain -h
+conda deactivate nextstrain-env
+```
+
+## NextStrain Analysis
+
+### Entry Point - IQTREE Phylogeny
+Follow the [Tuberculosis Tutorial](https://nextstrain.org/docs/tutorials/tb) picking up right after [Get the Topology](https://nextstrain.org/docs/tutorials/tb#get-the-topology).  
+
+**Fix Branch Lengths & Get a Time-Resolved Tree**  
+Adjusts branch lengths in the tree to position tips by their sample date and infer the most likely time of their ancestors, using TreeTime.
+```
+augur refine \
+    --tree ../testX/iqtree/iqtree.core-filter0_bootstrap.treefile \
+    --alignment ../testX/snippy_multi/snippy-core.full.filter0.fasta \
+    --vcf-reference ../testX/reference_genome/reference_genome\GCF_000009065.1_ASM906v1_genomic.fna \
+    --metadata test.tsv \
+    --timetree \
+    --root residual \
+    --coalescent opt \
+    --output-tree refine-tree.nwk \
+    --output-node-data refine-branch_lengths.json
+```