diff --git a/workflow/snakemake_rules/export_for_nextstrain.smk b/workflow/snakemake_rules/export_for_nextstrain.smk
index 01057da14..a7650656a 100644
--- a/workflow/snakemake_rules/export_for_nextstrain.smk
+++ b/workflow/snakemake_rules/export_for_nextstrain.smk
@@ -35,7 +35,6 @@ rule all_regions:
     input:
         auspice_json = expand("auspice/{prefix}_{build_name}.json", prefix=config["auspice_json_prefix"], build_name=BUILD_NAMES),
         tip_frequencies_json = expand("auspice/{prefix}_{build_name}_tip-frequencies.json", prefix=config["auspice_json_prefix"], build_name=BUILD_NAMES),
-        root_sequence_json = expand("auspice/{prefix}_{build_name}_root-sequence.json", prefix=config["auspice_json_prefix"], build_name=BUILD_NAMES),
         dated_auspice_json = expand("auspice/{prefix}_{build_name}_{date}.json", prefix=config["auspice_json_prefix"], build_name=BUILD_NAMES, date=config.get("build_date", get_todays_date())),
         dated_tip_frequencies_json = expand("auspice/{prefix}_{build_name}_{date}_tip-frequencies.json", prefix=config["auspice_json_prefix"], build_name=BUILD_NAMES, date=config.get("build_date", get_todays_date())),
         dated_root_sequence_json = expand("auspice/{prefix}_{build_name}_{date}_root-sequence.json", prefix=config["auspice_json_prefix"], build_name=BUILD_NAMES, date=config.get("build_date", get_todays_date()))
diff --git a/workflow/snakemake_rules/main_workflow.smk b/workflow/snakemake_rules/main_workflow.smk
index 82922157e..96b4d3886 100644
--- a/workflow/snakemake_rules/main_workflow.smk
+++ b/workflow/snakemake_rules/main_workflow.smk
@@ -1402,8 +1402,7 @@ rule export:
         lat_longs = config["files"]["lat_longs"],
         description = rules.build_description.output.description
     output:
-        auspice_json = "results/{build_name}/ncov_with_accessions.json",
-        root_sequence_json = "results/{build_name}/ncov_with_accessions_root-sequence.json"
+        auspice_json = "results/{build_name}/ncov_with_accessions.json"
     log:
         "logs/export_{build_name}.txt"
     benchmark:
@@ -1421,7 +1420,7 @@ rule export:
             --metadata {input.metadata} \
             --node-data {input.node_data} \
             --auspice-config {input.auspice_config} \
-            --include-root-sequence \
+            --include-root-sequence-inline \
             --colors {input.colors} \
             --lat-longs {input.lat_longs} \
             --title {params.title:q} \