diff --git a/ingest/bin/join-metadata-and-clades.py b/ingest/bin/join-metadata-and-clades.py
deleted file mode 100755
index 3a0e919e..00000000
--- a/ingest/bin/join-metadata-and-clades.py
+++ /dev/null
@@ -1,77 +0,0 @@
-#!/usr/bin/env python3
-import argparse
-import re
-import sys
-import pandas as pd
-
-NEXTCLADE_JOIN_COLUMN_NAME = 'seqName'
-VALUE_MISSING_DATA = '?'
-
-column_map = {
-    "clade": "clade",
-    "outbreak": "outbreak",
-    "lineage": "lineage",
-    "coverage": "coverage",
-    "totalMissing": "missing_data",
-    "totalSubstitutions": "divergence",
-    "totalNonACGTNs": "nonACGTN",
-    "qc.missingData.status": "QC_missing_data",
-    "qc.mixedSites.status": "QC_mixed_sites",
-    "qc.privateMutations.status": "QC_rare_mutations",
-    "qc.frameShifts.status": "QC_frame_shifts",
-    "qc.stopCodons.status": "QC_stop_codons",
-    "frameShifts": "frame_shifts",
-    "isReverseComplement": "is_reverse_complement",
-#    "deletions": "deletions",
-#    "insertions": "insertions"
-#    "substitutions": "substitutions",
-#    "aaSubstitutions": "aaSubstitutions"
-}
-
-
-def parse_args():
-    parser = argparse.ArgumentParser(
-        description="Joins metadata file with Nextclade clade output",
-    )
-    parser.add_argument("--metadata")
-    parser.add_argument("--nextclade")
-    parser.add_argument("--id-field")
-    parser.add_argument("-o", default=sys.stdout)
-    return parser.parse_args()
-
-def main():
-    args = parse_args()
-
-    metadata = pd.read_csv(args.metadata, index_col=args.id_field,
-                           sep='\t', low_memory=False, na_filter = False)
-
-    # Read and rename clade column to be more descriptive
-    clades = pd.read_csv(args.nextclade, index_col=NEXTCLADE_JOIN_COLUMN_NAME,
-                         sep='\t', low_memory=False, na_filter = False) \
-            .rename(columns=column_map)
-
-    clades.index = clades.index.map(lambda x: re.sub(" \|.*", "", x))
-
-    # Select columns in column map
-    clades = clades[list(column_map.values())]
-
-    # Separate long from short columns
-    short_metadata = metadata.iloc[:,:-2].copy()
-    long_metadata = metadata.iloc[:,-2:].copy()
-
-    # Concatenate on columns
-    result = pd.merge(
-        short_metadata, clades,
-        left_index=True,
-        right_index=True,
-        how='left'
-    )
-
-    # Add long columns to back
-    result = pd.concat([result, long_metadata], axis=1)
-
-    result.to_csv(args.o, index_label=args.id_field, sep='\t')
-
-
-if __name__ == '__main__':
-    main()
diff --git a/ingest/source-data/nextclade-field-map.tsv b/ingest/source-data/nextclade-field-map.tsv
new file mode 100644
index 00000000..41894fe9
--- /dev/null
+++ b/ingest/source-data/nextclade-field-map.tsv
@@ -0,0 +1,17 @@
+key	value
+index	index
+seqName	seqName
+clade	clade
+outbreak	outbreak
+lineage	lineage
+coverage	coverage
+totalMissing	missing_data
+totalSubstitutions	divergence
+totalNonACGTNs	nonACGTN
+qc.missingData.status	QC_missing_data
+qc.mixedSites.status	QC_mixed_sites
+qc.privateMutations.status	QC_rare_mutations
+qc.frameShifts.status	QC_frame_shifts
+qc.stopCodons.status	QC_stop_codons
+frameShifts	frame_shifts
+isReverseComplement	is_reverse_complement
\ No newline at end of file
diff --git a/ingest/workflow/snakemake_rules/nextclade.smk b/ingest/workflow/snakemake_rules/nextclade.smk
index 28da0a98..ceed8d68 100644
--- a/ingest/workflow/snakemake_rules/nextclade.smk
+++ b/ingest/workflow/snakemake_rules/nextclade.smk
@@ -56,15 +56,31 @@ rule join_metadata_clades:
     input:
         nextclade="data/nextclade.tsv",
         metadata="data/metadata_raw.tsv",
+        nextclade_field_map="source-data/nextclade-field-map.tsv",
     output:
-        "data/metadata.tsv",
+        metadata="data/metadata.tsv",
     params:
         id_field=config["transform"]["id_field"],
     shell:
         """
-        python3 bin/join-metadata-and-clades.py \
-                --id-field {params.id_field} \
-                --metadata {input.metadata} \
-                --nextclade {input.nextclade} \
-                -o {output}
+        csvtk -tl rename2 \
+            -F \
+            -f '*' \
+            -p '(.+)' \
+            -r '{{kv}}' \
+            -k {input.nextclade_field_map} \
+            {input.nextclade} \
+            > results/nextclade_renamed.tsv
+
+        export APPEND_FIELDS=`awk 'NR>1 {{print $2}}' {input.nextclade_field_map} | grep -v -e "index" -e "seqName" | tr '\n' ',' | sed 's/,\$//g'`
+
+        tsv-join -H \
+            --filter-file results/nextclade_renamed.tsv \
+            --key-fields seqName \
+            --data-fields {params.id_field} \
+            --append-fields $APPEND_FIELDS \
+            --allow-duplicate-keys \
+            --write-all ? \
+            {input.metadata} \
+            > {output.metadata}
         """