diff --git a/Snakefile b/Snakefile
index 98001979..8ec213aa 100644
--- a/Snakefile
+++ b/Snakefile
@@ -2,7 +2,9 @@ from packaging import version
 from augur.__version__ import __version__ as augur_version
 import sys
 
-min_augur_version = "16.0.0"
+# FIXME: Update version once Augur changes¹ are released.
+# ¹ https://github.com/nextstrain/augur/commit/9bf1b4ce4169b2a10ea974608188c2fdd918b9bc
+min_augur_version = "22.1.0"
 if version.parse(augur_version) < version.parse(min_augur_version):
     print("This pipeline needs a newer version of augur than you currently have...")
     print(
diff --git a/config/config_hmpxv1.yaml b/config/config_hmpxv1.yaml
index 33199c19..13c3a2d9 100644
--- a/config/config_hmpxv1.yaml
+++ b/config/config_hmpxv1.yaml
@@ -12,7 +12,7 @@ tree_mask: "config/tree_mask.tsv"
 # Use `accession` as the ID column since `strain` currently contains duplicates¹.
 # ¹ https://github.com/nextstrain/monkeypox/issues/33
 strain_id_field: "accession"
-display_strain_field: "strain_original"
+display_strain_field: "strain"
 
 build_name: "hmpxv1"
 auspice_name: "monkeypox_hmpxv1"
diff --git a/config/config_hmpxv1_big.yaml b/config/config_hmpxv1_big.yaml
index a2f0f295..d6a663f1 100644
--- a/config/config_hmpxv1_big.yaml
+++ b/config/config_hmpxv1_big.yaml
@@ -12,7 +12,7 @@ tree_mask: "config/tree_mask.tsv"
 # Use `accession` as the ID column since `strain` currently contains duplicates¹.
 # ¹ https://github.com/nextstrain/monkeypox/issues/33
 strain_id_field: "accession"
-display_strain_field: "strain_original"
+display_strain_field: "strain"
 
 build_name: "hmpxv1_big"
 auspice_name: "monkeypox_hmpxv1_big"
diff --git a/config/config_mpxv.yaml b/config/config_mpxv.yaml
index ec3b61a5..12a4e820 100644
--- a/config/config_mpxv.yaml
+++ b/config/config_mpxv.yaml
@@ -12,7 +12,7 @@ tree_mask: "config/tree_mask.tsv"
 # Use `accession` as the ID column since `strain` currently contains duplicates¹.
 # ¹ https://github.com/nextstrain/monkeypox/issues/33
 strain_id_field: "accession"
-display_strain_field: "strain_original"
+display_strain_field: "strain"
 
 build_name: "mpxv"
 auspice_name: "monkeypox_mpxv"
diff --git a/scripts/construct-recency-from-submission-date.py b/scripts/construct-recency-from-submission-date.py
index 4268dadf..24670b6d 100644
--- a/scripts/construct-recency-from-submission-date.py
+++ b/scripts/construct-recency-from-submission-date.py
@@ -38,10 +38,11 @@ def get_recency(date_str, ref_date):
     )
 
     parser.add_argument('--metadata', type=str, required=True, help="metadata file")
+    parser.add_argument('--metadata-id-columns', nargs="+", help="names of possible metadata columns containing identifier information, ordered by priority. Only one ID column will be inferred.")
     parser.add_argument('--output', type=str, required=True, help="output json")
     args = parser.parse_args()
 
-    meta = read_metadata(args.metadata).to_dict(orient="index")
+    meta = read_metadata(args.metadata, id_columns=args.metadata_id_columns).to_dict(orient="index")
 
     node_data = {'nodes':{}}
     ref_date = datetime.now()
diff --git a/scripts/set_final_strain_name.py b/scripts/set_final_strain_name.py
index 0036f2a5..08ca9359 100644
--- a/scripts/set_final_strain_name.py
+++ b/scripts/set_final_strain_name.py
@@ -1,5 +1,6 @@
 import pandas as pd
 import json, argparse
+from augur.io import read_metadata
 
 def replace_name_recursive(node, lookup):
     if node["name"] in lookup:
@@ -17,14 +18,15 @@ def replace_name_recursive(node, lookup):
 
     parser.add_argument('--input-auspice-json', type=str, required=True, help="input auspice_json")
     parser.add_argument('--metadata', type=str, required=True, help="input data")
+    parser.add_argument('--metadata-id-columns', nargs="+", help="names of possible metadata columns containing identifier information, ordered by priority. Only one ID column will be inferred.")
     parser.add_argument('--display-strain-name', type=str, required=True, help="field to use as strain name in auspice")
     parser.add_argument('--output', type=str, metavar="JSON", required=True, help="output Auspice JSON")
     args = parser.parse_args()
 
-    metadata = pd.read_csv(args.metadata, sep='\t')
+    metadata = read_metadata(args.metadata, id_columns=args.metadata_id_columns)
     name_lookup = {}
     for ri, row in metadata.iterrows():
-        strain_id = row['strain']
+        strain_id = row.name
         name_lookup[strain_id] = args.display_strain_name if pd.isna(row[args.display_strain_name]) else row[args.display_strain_name]
 
     with open(args.input_auspice_json, 'r') as fh:
diff --git a/workflow/snakemake_rules/core.smk b/workflow/snakemake_rules/core.smk
index 8b14e81b..51c68124 100644
--- a/workflow/snakemake_rules/core.smk
+++ b/workflow/snakemake_rules/core.smk
@@ -13,20 +13,6 @@ In addition, `build_dir` and `auspice_dir` need to be defined upstream.
 """
 
 
-rule wrangle_metadata:
-    input:
-        metadata="data/metadata.tsv",
-    output:
-        metadata="results/metadata.tsv",
-    params:
-        strain_id=config["strain_id_field"],
-    shell:
-        """
-        csvtk -t rename -f strain -n strain_original {input.metadata} \
-            | csvtk mutate -t -f {params.strain_id} -n strain > {output.metadata}
-        """
-
-
 rule exclude_bad:
     message:
         """
@@ -37,7 +23,7 @@ rule exclude_bad:
         """
     input:
         sequences="data/sequences.fasta",
-        metadata="results/metadata.tsv",
+        metadata="data/metadata.tsv",
         exclude=config["exclude"],
     output:
         sequences=build_dir + "/{build_name}/good_sequences.fasta",
@@ -46,11 +32,13 @@ rule exclude_bad:
     params:
         min_date=config["min_date"],
         min_length=config["min_length"],
+        strain_id=config["strain_id_field"],
     shell:
         """
         augur filter \
             --sequences {input.sequences} \
             --metadata {input.metadata} \
+            --metadata-id-columns {params.strain_id} \
             --exclude {input.exclude} \
             --output-sequences {output.sequences} \
             --output-metadata {output.metadata} \
@@ -93,11 +81,13 @@ rule filter:
         group_by=config.get("group_by", "--group-by clade lineage"),
         sequences_per_group=config["sequences_per_group"],
         other_filters=config.get("filters", ""),
+        strain_id=config["strain_id_field"],
     shell:
         """
         augur filter \
             --sequences {input.sequences} \
             --metadata {input.metadata} \
+            --metadata-id-columns {params.strain_id} \
             --include {input.include} \
             --output-sequences {output.sequences} \
             --output-metadata {output.metadata} \
@@ -246,12 +236,14 @@ rule refine:
         clock_std_dev=f"--clock-std-dev {config['clock_std_dev']}"
         if "clock_std_dev" in config
         else "",
+        strain_id=config["strain_id_field"],
     shell:
         """
         augur refine \
             --tree {input.tree} \
             --alignment {input.alignment} \
             --metadata {input.metadata} \
+            --metadata-id-columns {params.strain_id} \
             --output-tree {output.tree} \
             --timetree \
             --root {params.root} \
@@ -320,11 +312,13 @@ rule traits:
     params:
         columns="country",
         sampling_bias_correction=3,
+        strain_id=config["strain_id_field"],
     shell:
         """
         augur traits \
             --tree {input.tree} \
             --metadata {input.metadata} \
+            --metadata-id-columns {params.strain_id} \
             --output {output.node_data} \
             --columns {params.columns} \
             --confidence \
@@ -400,10 +394,13 @@ rule recency:
         metadata=build_dir + "/{build_name}/metadata.tsv",
     output:
         node_data=build_dir + "/{build_name}/recency.json",
+    params:
+        strain_id=config["strain_id_field"],
     shell:
         """
         python3 scripts/construct-recency-from-submission-date.py \
             --metadata {input.metadata} \
+            --metadata-id-columns {params.strain_id} \
             --output {output} 2>&1
         """
 
@@ -447,11 +444,14 @@ rule export:
     output:
         auspice_json=build_dir + "/{build_name}/raw_tree.json",
         root_sequence=build_dir + "/{build_name}/raw_tree_root-sequence.json",
+    params:
+        strain_id=config["strain_id_field"],
     shell:
         """
         augur export v2 \
             --tree {input.tree} \
             --metadata {input.metadata} \
+            --metadata-id-columns {params.strain_id} \
             --node-data {input.branch_lengths} {input.nt_muts} {input.aa_muts} {input.mutation_context} {input.clades} {input.recency}\
             --colors {input.colors} \
             --lat-longs {input.lat_longs} \
@@ -471,10 +471,12 @@ rule final_strain_name:
         auspice_json=build_dir + "/{build_name}/tree.json",
         root_sequence=build_dir + "/{build_name}/tree_root-sequence.json",
     params:
+        strain_id=config["strain_id_field"],
         display_strain_field=config.get("display_strain_field", "strain"),
     shell:
         """
         python3 scripts/set_final_strain_name.py --metadata {input.metadata} \
+                --metadata-id-columns {params.strain_id} \
                 --input-auspice-json {input.auspice_json} \
                 --display-strain-name {params.display_strain_field} \
                 --output {output.auspice_json}