diff --git a/src/main/java/CommandLineInterface.java b/src/main/java/CommandLineInterface.java
index 230e57b..ee56302 100644
--- a/src/main/java/CommandLineInterface.java
+++ b/src/main/java/CommandLineInterface.java
@@ -146,7 +146,17 @@ public class CommandLineInterface {
                 CellSample cells = getCells(cellFilename);
                 //get plate
                 Plate plate = getPlate(plateFilename);
-                GraphWithMapData graph = Simulator.makeGraph(cells, plate, 1, 0.0, 0.0, false);
+                GraphWithMapData graph;
+                if(line.hasOption("rd")){
+                    String[] readDepthArgs = line.getOptionValues("rd");
+                    Integer readDepth = Integer.parseInt(readDepthArgs[0]);
+                    Double readErrorRate = Double.parseDouble(readDepthArgs[1]);
+                    Double errorCollisionRate = Double.parseDouble(readDepthArgs[2]);
+                    graph = Simulator.makeGraph(cells, plate, readDepth, readErrorRate, errorCollisionRate, false);
+                }
+                else{
+                    graph = Simulator.makeGraph(cells, plate, 1, 0.0, 0.0, false);
+                }
                 if (!line.hasOption("no-binary")) { //output binary file unless told not to
                     GraphDataObjectWriter writer = new GraphDataObjectWriter(outputFilename, graph, false);
                     writer.writeDataToFile();
@@ -388,11 +398,18 @@ public class CommandLineInterface {
                 .longOpt("no-binary")
                 .desc("(Optional) Don't output serialized binary file")
                 .build();
+        Option simulateReadDepth = Option.builder("rd")
+                .longOpt("read-depth")
+                .desc("(Optional) Simulate read depth and read errors. Has three arguments: the read depth (integer >= 1), the read error probability (0.0 - 1.0), and the error collision probability (0.0 - 1.0)")
+                .hasArgs()
+                .numberOfArgs(3)
+                .build();
         graphOptions.addOption(cellFilename);
         graphOptions.addOption(plateFilename);
         graphOptions.addOption(outputFileOption());
         graphOptions.addOption(outputGraphML);
         graphOptions.addOption(outputSerializedBinary);
+        graphOptions.addOption(simulateReadDepth);
         return graphOptions;
     }