added update --outdir to readme

andersen-lab · Feb 16, 2022 · 9b1be8b · 9b1be8b
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commit 9b1be8b
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/README.md b/README.md
@@ -58,7 +58,7 @@ By default, this method ships with an existing "data/usher_barcodes.csv" file fo
 ```
 freyja update
 ```
-which downloads new versions of the curated lineage file as well as the UShER global phylogenetic [tree](http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/), which is subsequently converted into barcodes and saved in "data/usher_barcodes.csv".
+which downloads new versions of the curated lineage file as well as the UShER global phylogenetic [tree](http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/), which is subsequently converted into barcodes and saved in "data/usher_barcodes.csv". The ```--outdir``` option can be used to specify a local directory to store the lineage mapping and barcode files. 
 
 We now provide a fast bootstrapping method for freyja, which can be run using the command