diff --git a/ingest/Snakefile b/ingest/Snakefile
index 4e829ea4..6675ffe0 100644
--- a/ingest/Snakefile
+++ b/ingest/Snakefile
@@ -70,7 +70,6 @@ rule all:
 
 include: "workflow/snakemake_rules/fetch_sequences.smk"
 include: "workflow/snakemake_rules/transform.smk"
-include: "workflow/snakemake_rules/nextclade.smk"
 
 
 if config.get("upload", False):
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/workflow/snakemake_rules/nextclade.smk b/ingest/workflow/snakemake_rules/nextclade.smk
deleted file mode 100644
index 28da0a98..00000000
--- a/ingest/workflow/snakemake_rules/nextclade.smk
+++ /dev/null
@@ -1,70 +0,0 @@
-
-rule nextclade_dataset:
-    output:
-        temp("mpxv.zip"),
-    shell:
-        """
-        nextclade dataset get --name MPXV --output-zip {output}
-        """
-
-
-rule nextclade_dataset_hMPXV:
-    output:
-        temp("hmpxv.zip"),
-    shell:
-        """
-        nextclade dataset get --name hMPXV --output-zip {output}
-        """
-
-
-rule align:
-    input:
-        sequences="data/sequences.fasta",
-        dataset="hmpxv.zip",
-    output:
-        alignment="data/alignment.fasta",
-        insertions="data/insertions.csv",
-        translations="data/translations.zip",
-    params:
-        # The lambda is used to deactivate automatic wildcard expansion.
-        # https://github.com/snakemake/snakemake/blob/384d0066c512b0429719085f2cf886fdb97fd80a/snakemake/rules.py#L997-L1000
-        translations=lambda w: "data/translations/{gene}.fasta",
-    threads: 4
-    shell:
-        """
-        nextclade run -D {input.dataset} -j {threads}   --retry-reverse-complement \
-                  --output-fasta {output.alignment}  --output-translations {params.translations} \
-                  --output-insertions {output.insertions} {input.sequences}
-        zip -rj {output.translations} data/translations
-        """
-
-
-rule nextclade:
-    input:
-        sequences="data/sequences.fasta",
-        dataset="mpxv.zip",
-    output:
-        "data/nextclade.tsv",
-    threads: 4
-    shell:
-        """
-        nextclade run -D {input.dataset} -j {threads} --output-tsv {output}  {input.sequences}  --retry-reverse-complement
-        """
-
-
-rule join_metadata_clades:
-    input:
-        nextclade="data/nextclade.tsv",
-        metadata="data/metadata_raw.tsv",
-    output:
-        "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}
-        """
diff --git a/ingest/workflow/snakemake_rules/transform.smk b/ingest/workflow/snakemake_rules/transform.smk
index a39fb735..1c0cea5a 100644
--- a/ingest/workflow/snakemake_rules/transform.smk
+++ b/ingest/workflow/snakemake_rules/transform.smk
@@ -42,7 +42,7 @@ rule transform:
         all_geolocation_rules="data/all-geolocation-rules.tsv",
         annotations=config["transform"]["annotations"],
     output:
-        metadata="data/metadata_raw.tsv",
+        metadata="data/metadata.tsv",
         sequences="data/sequences.fasta",
     log:
         "logs/transform.txt",