diff --git a/eva-accession-release/src/main/java/uk/ac/ebi/eva/accession/release/io/ContigWriter.java b/eva-accession-release/src/main/java/uk/ac/ebi/eva/accession/release/io/ContigWriter.java
index 45420f17b..916a85a5f 100644
--- a/eva-accession-release/src/main/java/uk/ac/ebi/eva/accession/release/io/ContigWriter.java
+++ b/eva-accession-release/src/main/java/uk/ac/ebi/eva/accession/release/io/ContigWriter.java
@@ -23,9 +23,11 @@
 import uk.ac.ebi.eva.accession.core.contig.ContigNaming;
 import uk.ac.ebi.eva.accession.core.contig.ContigSynonyms;
 
+import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
+import java.io.InputStreamReader;
 import java.io.PrintWriter;
 import java.nio.file.Paths;
 import java.util.List;
@@ -69,6 +71,30 @@ public void update(ExecutionContext executionContext) throws ItemStreamException
     @Override
     public void close() throws ItemStreamException {
         printWriter.close();
+        sortContigFile();
+    }
+
+    private void sortContigFile() {
+        try {
+            Process process = Runtime.getRuntime().exec(new String[]{"sort", this.output.getAbsolutePath()});
+            int exitCode = process.waitFor();
+
+            if (exitCode != 0) {
+                throw new ItemStreamException(
+                        "Trying to sort the contig list, the 'sort' command returned exit code'" + exitCode + "'.");
+            }
+
+            BufferedReader br = new BufferedReader(new InputStreamReader(process.getInputStream()));
+            String line;
+            PrintWriter printWriter2 = new PrintWriter(new FileWriter(this.output));
+            while ((line = br.readLine()) != null) {
+                printWriter2.println(line);
+            }
+            printWriter2.close();
+
+        } catch (IOException | InterruptedException e) {
+            throw new ItemStreamException("Failed sorting contig list. ", e);
+        }
     }
 
     @Override
@@ -85,7 +111,7 @@ public void write(List<? extends String> contigs) {
                 throw new IllegalArgumentException("Could not find the corresponding sequence name for contig " + contig);
             }
 
-            printWriter.println(contig + "," + sequenceName);
+            printWriter.println(sequenceName + "," + contig);
         }
     }
 
diff --git a/eva-accession-release/src/main/java/uk/ac/ebi/eva/accession/release/io/VariantContextWriter.java b/eva-accession-release/src/main/java/uk/ac/ebi/eva/accession/release/io/VariantContextWriter.java
index 437287d80..c4bdd4b5f 100644
--- a/eva-accession-release/src/main/java/uk/ac/ebi/eva/accession/release/io/VariantContextWriter.java
+++ b/eva-accession-release/src/main/java/uk/ac/ebi/eva/accession/release/io/VariantContextWriter.java
@@ -137,9 +137,9 @@ private void addContigs(Set<VCFHeaderLine> metaData) {
             BufferedReader bufferedReader = new BufferedReader(new FileReader(contigsFilePath));
             String contigLine;
             while ((contigLine = bufferedReader.readLine()) != null) {
-                String[] contigAndName = contigLine.split(",");
-                String contig = contigAndName[0];
-                String name = contigAndName[1];
+                String[] nameAndContig = contigLine.split(",");
+                String name = nameAndContig[0];
+                String contig = nameAndContig[1];
                 metaData.add(new VCFHeaderLine("contig", "<ID=" + name + ",accession=\"" + contig + "\">"));
             }
         } catch (IOException e) {
diff --git a/eva-accession-release/src/test/java/uk/ac/ebi/eva/accession/release/configuration/steps/ListActiveContigsStepConfigurationTest.java b/eva-accession-release/src/test/java/uk/ac/ebi/eva/accession/release/configuration/steps/ListActiveContigsStepConfigurationTest.java
index 8c8d78f2d..174841fd7 100644
--- a/eva-accession-release/src/test/java/uk/ac/ebi/eva/accession/release/configuration/steps/ListActiveContigsStepConfigurationTest.java
+++ b/eva-accession-release/src/test/java/uk/ac/ebi/eva/accession/release/configuration/steps/ListActiveContigsStepConfigurationTest.java
@@ -100,7 +100,7 @@ public void assertStepExecutesAndCompletes() {
     public void contigsWritten() throws Exception {
         assertStepExecutesAndCompletes();
 
-        assertEquals(new HashSet<>(Arrays.asList("CM001954.1,CAE13", "CM001941.2,CAE1")),
+        assertEquals(new HashSet<>(Arrays.asList("CAE13,CM001954.1", "CAE1,CM001941.2")),
                      setOfLines(getActiveContigsFilePath(inputParameters.getOutputFolder(),
                                                          inputParameters.getAssemblyAccession())));
     }
diff --git a/eva-accession-release/src/test/java/uk/ac/ebi/eva/accession/release/configuration/steps/ListMergedContigsStepConfigurationTest.java b/eva-accession-release/src/test/java/uk/ac/ebi/eva/accession/release/configuration/steps/ListMergedContigsStepConfigurationTest.java
index 18cd449bd..6d9c1d988 100644
--- a/eva-accession-release/src/test/java/uk/ac/ebi/eva/accession/release/configuration/steps/ListMergedContigsStepConfigurationTest.java
+++ b/eva-accession-release/src/test/java/uk/ac/ebi/eva/accession/release/configuration/steps/ListMergedContigsStepConfigurationTest.java
@@ -101,7 +101,7 @@ public void assertStepExecutesAndCompletes() {
     public void contigsWritten() throws Exception {
         assertStepExecutesAndCompletes();
 
-        assertEquals(new HashSet<>(Arrays.asList("CM001954.1,CAE13", "CM001941.2,CAE1")),
+        assertEquals(new HashSet<>(Arrays.asList("CAE13,CM001954.1", "CAE1,CM001941.2")),
                      setOfLines(ContigWriter.getMergedContigsFilePath(inputParameters.getOutputFolder(),
                                                                       inputParameters.getAssemblyAccession())));
     }
diff --git a/eva-accession-release/src/test/java/uk/ac/ebi/eva/accession/release/io/ContigWriterTest.java b/eva-accession-release/src/test/java/uk/ac/ebi/eva/accession/release/io/ContigWriterTest.java
index d319330ad..33b0a096c 100644
--- a/eva-accession-release/src/test/java/uk/ac/ebi/eva/accession/release/io/ContigWriterTest.java
+++ b/eva-accession-release/src/test/java/uk/ac/ebi/eva/accession/release/io/ContigWriterTest.java
@@ -85,8 +85,8 @@ public void write() throws Exception {
 
         assertEquals(contigs.size(), numberOfLines(output));
 
-        List<String> expectedLines = Arrays.asList("CM0001.1,Chr1", "CM0002.1,Chr2", "CM0003.1,Chr3");
-        assertContigFileContent(output, expectedLines);
+        List<String> expectedLinesSorted = Arrays.asList("Chr1,CM0001.1", "Chr2,CM0002.1", "Chr3,CM0003.1");
+        assertContigFileContentAndOrder(output, expectedLinesSorted);
     }
 
     private long numberOfLines(File file) throws IOException {
@@ -94,11 +94,13 @@ private long numberOfLines(File file) throws IOException {
         return br.lines().count();
     }
 
-    private void assertContigFileContent(File file, List<String> expectedLines) throws IOException {
+    private void assertContigFileContentAndOrder(File file, List<String> expectedLines) throws IOException {
         BufferedReader br = new BufferedReader(new FileReader(file));
+        int index = 0;
         String line;
         while ((line = br.readLine()) != null) {
-            assertTrue(expectedLines.contains(line));
+            assertEquals(expectedLines.get(index), line);
+            index++;
         }
     }
 
@@ -117,14 +119,14 @@ public void useSequenceNameIfContigIsRefSeqAccession() throws IOException {
         ContigWriter contigWriter = new ContigWriter(output, contigMapping);
 
         contigWriter.open(null);
-        List<String> contigs = Arrays.asList(REFSEQ_ACCESSION_1, REFSEQ_ACCESSION_2, GENBANK_ACCESSION_3);
+        List<String> contigs = Arrays.asList(REFSEQ_ACCESSION_2, GENBANK_ACCESSION_3, REFSEQ_ACCESSION_1);
         contigWriter.write(contigs);
         contigWriter.close();
 
         assertEquals(contigs.size(), numberOfLines(output));
 
-        List<String> expectedLines = Arrays.asList("NC0001.1,Chr1", "NC0002.1,Chr2", "CM0003.1,Chr3");
-        assertContigFileContent(output, expectedLines);
+        List<String> expectedLinesSorted = Arrays.asList("Chr1,NC0001.1", "Chr2,NC0002.1", "Chr3,CM0003.1");
+        assertContigFileContentAndOrder(output, expectedLinesSorted);
     }
 
     /**
diff --git a/eva-accession-release/src/test/java/uk/ac/ebi/eva/accession/release/io/VariantContextWriterTest.java b/eva-accession-release/src/test/java/uk/ac/ebi/eva/accession/release/io/VariantContextWriterTest.java
index f4ec73b03..d0d14e0f4 100644
--- a/eva-accession-release/src/test/java/uk/ac/ebi/eva/accession/release/io/VariantContextWriterTest.java
+++ b/eva-accession-release/src/test/java/uk/ac/ebi/eva/accession/release/io/VariantContextWriterTest.java
@@ -187,7 +187,7 @@ private List<String> grepFile(File file, String regex) throws IOException {
     public void checkMetadataSection() throws Exception {
         File outputFolder = temporaryFolder.newFolder();
         FileWriter fileWriter = new FileWriter(ContigWriter.getActiveContigsFilePath(outputFolder, REFERENCE_ASSEMBLY));
-        String contig = "CM0001.1,Chr1";
+        String contig = "Chr1,CM0001.1";
         fileWriter.write(contig);
         fileWriter.close();