diff --git a/Snakefile b/Snakefile
index 3562078..4f7dbfe 100644
--- a/Snakefile
+++ b/Snakefile
@@ -1,3 +1,6 @@
+if not config:
+    configfile: "config/config_zika.yaml"
+
 rule all:
     input:
         auspice_json = "auspice/zika.json",
@@ -59,12 +62,14 @@ rule filter:
         group_by = "country year month",
         sequences_per_group = 40,
         min_date = 2012,
-        min_length = 5385
+        min_length = 5385,
+        strain_id = config.get("strain_id_field", "strain"),
     shell:
         """
         augur filter \
             --sequences {input.sequences} \
             --metadata {input.metadata} \
+            --metadata-id-columns {params.strain_id} \
             --exclude {input.exclude} \
             --output {output.sequences} \
             --group-by {params.group_by} \
@@ -124,13 +129,15 @@ rule refine:
     params:
         coalescent = "opt",
         date_inference = "marginal",
-        clock_filter_iqd = 4
+        clock_filter_iqd = 4,
+        strain_id = config.get("strain_id_field", "strain"),
     shell:
         """
         augur refine \
             --tree {input.tree} \
             --alignment {input.alignment} \
             --metadata {input.metadata} \
+            --metadata-id-columns {params.strain_id} \
             --output-tree {output.tree} \
             --output-node-data {output.node_data} \
             --timetree \
@@ -212,12 +219,15 @@ rule export:
         auspice_config = files.auspice_config,
         description = files.description
     output:
-        auspice_json = rules.all.input.auspice_json
+        auspice_json = rules.all.input.auspice_json,
+    params:
+        strain_id = config.get("strain_id_field", "strain"),
     shell:
         """
         augur export v2 \
             --tree {input.tree} \
             --metadata {input.metadata} \
+            --metadata-id-columns {params.strain_id} \
             --node-data {input.branch_lengths} {input.traits} {input.nt_muts} {input.aa_muts} \
             --colors {input.colors} \
             --auspice-config {input.auspice_config} \
diff --git a/config/config_zika.yaml b/config/config_zika.yaml
new file mode 100644
index 0000000..5345584
--- /dev/null
+++ b/config/config_zika.yaml
@@ -0,0 +1,2 @@
+strain_id_field: "genbank_accession"
+display_strain_field: "strain"
\ No newline at end of file