diff --git a/src/main/java/uk/ac/ebi/embl/api/validation/submission/Context.java b/src/main/java/uk/ac/ebi/embl/api/validation/submission/Context.java
index c9f1afcf..4b7e7811 100644
--- a/src/main/java/uk/ac/ebi/embl/api/validation/submission/Context.java
+++ b/src/main/java/uk/ac/ebi/embl/api/validation/submission/Context.java
@@ -15,7 +15,7 @@
 import uk.ac.ebi.embl.api.validation.submission.SubmissionFile.FileType;
 
 public enum Context {
-  sequence(FileType.FLATFILE, FileType.TSV),
+  sequence(FileType.FLATFILE, FileType.TSV, FileType.FASTA),
   transcriptome(FileType.FASTA, FileType.FLATFILE, FileType.MASTER),
   genome(
       FileType.FASTA,
diff --git a/src/main/java/uk/ac/ebi/embl/api/validation/submission/SubmissionValidator.java b/src/main/java/uk/ac/ebi/embl/api/validation/submission/SubmissionValidator.java
index e323b143..9992090b 100644
--- a/src/main/java/uk/ac/ebi/embl/api/validation/submission/SubmissionValidator.java
+++ b/src/main/java/uk/ac/ebi/embl/api/validation/submission/SubmissionValidator.java
@@ -341,6 +341,28 @@ private SubmissionFiles setSequenceOptions(SequenceManifest manifest) {
                         file.getFile(),
                         new File(file.getFile() + SequenceEntryUtils.FIXED_FILE_SUFFIX),
                         file.getReportFile())));
+    manifest
+        .files()
+        .get(SequenceManifest.FileType.SAMPLE_TSV)
+        .forEach(
+            file ->
+                submissionFiles.addFile(
+                    new SubmissionFile(
+                        SubmissionFile.FileType.TSV,
+                        file.getFile(),
+                        new File(file.getFile() + SequenceEntryUtils.FIXED_FILE_SUFFIX),
+                        file.getReportFile())));
+    manifest
+        .files()
+        .get(SequenceManifest.FileType.TAX_TSV)
+        .forEach(
+            file ->
+                submissionFiles.addFile(
+                    new SubmissionFile(
+                        SubmissionFile.FileType.TSV,
+                        file.getFile(),
+                        new File(file.getFile() + SequenceEntryUtils.FIXED_FILE_SUFFIX),
+                        file.getReportFile())));
     return submissionFiles;
   }