diff --git a/src/main/java/CommandLineInterface.java b/src/main/java/CommandLineInterface.java
index ee56302..e3d73ee 100644
--- a/src/main/java/CommandLineInterface.java
+++ b/src/main/java/CommandLineInterface.java
@@ -147,16 +147,19 @@ public class CommandLineInterface {
                 //get plate
                 Plate plate = getPlate(plateFilename);
                 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);
+                Integer readDepth = 1;
+                Double readErrorRate = 0.0;
+                Double errorCollisionRate = 0.0;
+                if (line.hasOption("rd")) {
+                    readDepth = Integer.parseInt(line.getOptionValue("rd"));
                 }
-                else{
-                    graph = Simulator.makeGraph(cells, plate, 1, 0.0, 0.0, false);
+                if (line.hasOption("err")) {
+                    readErrorRate = Double.parseDouble(line.getOptionValue("err"));
                 }
+                if (line.hasOption("coll")) {
+                    errorCollisionRate = Double.parseDouble(line.getOptionValue("coll"));
+                }
+                graph = Simulator.makeGraph(cells, plate, readDepth, readErrorRate, errorCollisionRate, false);
                 if (!line.hasOption("no-binary")) { //output binary file unless told not to
                     GraphDataObjectWriter writer = new GraphDataObjectWriter(outputFilename, graph, false);
                     writer.writeDataToFile();
@@ -398,18 +401,32 @@ public class CommandLineInterface {
                 .longOpt("no-binary")
                 .desc("(Optional) Don't output serialized binary file")
                 .build();
-        Option simulateReadDepth = Option.builder("rd")
+        Option readDepth = 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)
+                .desc("(Optional) The number of times to read each sequence.")
+                .hasArg()
+                .argName("depth")
+                .build();
+        Option readErrorProb = Option.builder("err")
+                .longOpt("read-error-prob")
+                .desc("(Optional) The probability that a sequence will be misread. (0.0 - 1.0)")
+                .hasArg()
+                .argName("prob")
+                .build();
+        Option errorCollisionProb = Option.builder("coll")
+                .longOpt("error-collision-prob")
+                .desc("(Optional) The probability that two misreads will produce the same spurious sequence. (0.0 - 1.0)")
+                .hasArg()
+                .argName("prob")
                 .build();
         graphOptions.addOption(cellFilename);
         graphOptions.addOption(plateFilename);
         graphOptions.addOption(outputFileOption());
         graphOptions.addOption(outputGraphML);
         graphOptions.addOption(outputSerializedBinary);
-        graphOptions.addOption(simulateReadDepth);
+        graphOptions.addOption(readDepth);
+        graphOptions.addOption(readErrorProb);
+        graphOptions.addOption(errorCollisionProb);
         return graphOptions;
     }