diff --git a/ingest/bin/upload-to-s3 b/ingest/bin/upload-to-s3
deleted file mode 100755
index 7ea4e6f..0000000
--- a/ingest/bin/upload-to-s3
+++ /dev/null
@@ -1,56 +0,0 @@
-#!/bin/bash
-# Originally copied from nextstrain/ncov-ingest repo
-set -euo pipefail
-
-bin="$(dirname "$0")"
-
-main() {
-    local src="${1:?A source file is required as the first argument.}"
-    local dst="${2:?A destination s3:// URL is required as the second argument.}"
-    local cloudfront_domain="${3:-}"
-
-    local s3path="${dst#s3://}"
-    local bucket="${s3path%%/*}"
-    local key="${s3path#*/}"
-
-    local src_hash dst_hash no_hash=0000000000000000000000000000000000000000000000000000000000000000
-    src_hash="$("$bin/sha256sum" < "$src")"
-    dst_hash="$(aws s3api head-object --bucket "$bucket" --key "$key" --query Metadata.sha256sum --output text 2>/dev/null || echo "$no_hash")"
-
-    if [[ $src_hash != "$dst_hash" ]]; then
-        # The record count may have changed
-        src_record_count="$(wc -l < "$src")"
-
-        echo "Uploading $src → $dst"
-        if [[ "$dst" == *.gz ]]; then
-            gzip -c "$src"
-        elif  [[ "$dst" == *.xz ]]; then
-            xz -2 -T0 -c "$src"
-        else
-            cat "$src"
-        fi | aws s3 cp --no-progress - "$dst" --metadata sha256sum="$src_hash",recordcount="$src_record_count" "$(content-type "$dst")"
-
-        if [[ -n $cloudfront_domain ]]; then
-            echo "Creating CloudFront invalidation for $cloudfront_domain/$key"
-            if ! "$bin"/cloudfront-invalidate "$cloudfront_domain" "/$key"; then
-                echo "CloudFront invalidation failed, but exiting with success anyway."
-            fi
-        fi
-
-    else
-        echo "Uploading $src → $dst: files are identical, skipping upload"
-    fi
-}
-
-content-type() {
-    case "$1" in
-        *.tsv)      echo --content-type=text/tab-separated-values;;
-        *.csv)      echo --content-type=text/comma-separated-values;;
-        *.ndjson)   echo --content-type=application/x-ndjson;;
-        *.gz)       echo --content-type=application/gzip;;
-        *.xz)       echo --content-type=application/x-xz;;
-        *)          echo --content-type=text/plain;;
-    esac
-}
-
-main
diff --git a/ingest/workflow/snakemake_rules/upload.smk b/ingest/workflow/snakemake_rules/upload.smk
index 36fddf9..b1bdcaf 100644
--- a/ingest/workflow/snakemake_rules/upload.smk
+++ b/ingest/workflow/snakemake_rules/upload.smk
@@ -21,5 +21,5 @@ rule upload_to_s3:
         cloudfront_domain = config["upload"].get("s3", {}).get("cloudfront_domain", "")
     shell:
         """
-        ./bin/upload-to-s3 {input:q} {params.s3_dst:q}/{wildcards.remote_file_name:q} {params.cloudfront_domain}
+        ./vendored/upload-to-s3 --quiet {input:q} {params.s3_dst:q}/{wildcards.remote_file_name:q} {params.cloudfront_domain}
         """