diff --git a/deep_sequencing_unit/.gitignore b/deep_sequencing_unit/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..21b51eb8ea0e846032679e8df364c5f9dd402afd
--- /dev/null
+++ b/deep_sequencing_unit/.gitignore
@@ -0,0 +1,5 @@
+/.shredder
+/.settings
+/test-output
+/temp-testng-customsuite.xml
+/targets
diff --git a/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/plugins/.gitignore b/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/plugins/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..c08e0e25cf3435f7585bf9cd40e2971117c24f33
--- /dev/null
+++ b/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/plugins/.gitignore
@@ -0,0 +1 @@
+/IlluminaSummaryXMLLoaderTestSpeed.java