diff --git a/src/main/java/CommandLineInterface.java b/src/main/java/CommandLineInterface.java
index a6d84b0..ea5ca23 100644
--- a/src/main/java/CommandLineInterface.java
+++ b/src/main/java/CommandLineInterface.java
@@ -197,7 +197,9 @@ public class CommandLineInterface {
 
     private static Options buildMainOptions() {
         Options mainOptions = new Options();
-        Option help = Option.builder("help").build();
+        Option help = Option.builder("help")
+                .desc("Displays this help menu")
+                .build();
         Option makeCells = Option.builder("cells")
                 .longOpt("make-cells")
                 .desc("Makes a cell sample file of distinct T cells")
@@ -292,21 +294,19 @@ public class CommandLineInterface {
         OptionGroup wellPopOptions = new OptionGroup(); // add this to plate options
         wellPopOptions.setRequired(true);
         Option randomWellPopulations = Option.builder("random")
-                .desc("Randomize well populations on sample plate.")
+                .desc("Randomize well populations on sample plate. Takes two arguments: the minimum possible population and the maximum possible population.")
                 .hasArgs()
                 .numberOfArgs(2)
-                .argName("max_pop min_pop")
+                .argName("minimum maximum")
                 .build();
         Option specificWellPopulations = Option.builder("pop")
-                .longOpt("populations")
-                .desc("The well populations for each section of the sample plate. There will be as many sections as populations given.")
+                .desc("The well populations for each section of the sample plate. There will be as many sections as there are populations given.")
                 .hasArgs()
-                .argName("1st_pop [2nd_pop]...")
+                .argName("number [number]...")
                 .build();
         Option dropoutRate = Option.builder("err") //add this to plate options
-                .longOpt("dropout-rate")
                 .hasArg()
-                .desc("The sequence dropout rate due to amplification error")
+                .desc("The sequence dropout rate due to amplification error. (0.0 - 1.0)")
                 .argName("rate")
                 .required()
                 .build();
@@ -355,33 +355,29 @@ public class CommandLineInterface {
         Options matchCDR3options = new Options();
         Option graphFilename = Option.builder("g")
                 .longOpt("graph-file")
-                .desc("Graph/data file to use")
+                .desc("The graph/data file to use")
                 .hasArg()
                 .argName("filename")
                 .required().build();
         Option minOccupancyOverlap = Option.builder("min")
-                .longOpt("min-overlap-size")
                 .desc("The minimum number of shared wells to attempt to match a sequence pair")
                 .hasArg()
-                .argName("minimum")
+                .argName("number")
                 .required().build();
         Option maxOccupancyOverlap = Option.builder("max")
-                .longOpt("max_overlap_size")
                 .desc("The maximum number of shared wells to attempt to match a sequence pair")
                 .hasArg()
-                .argName("maximum")
+                .argName("number")
                 .required().build();
         Option minOverlapPercent = Option.builder("minpct")
-                .longOpt("min-overlap-percent")
                 .desc("(Optional) The minimum percentage of a sequence's total occupancy shared by another sequence to attempt matching. (0 - 100) ")
                 .hasArg()
-                .argName("minimum")
+                .argName("percent")
                 .build();
         Option maxOccupancyDifference = Option.builder("maxdiff")
-                .longOpt("max-occupancy-difference")
                 .desc("(Optional) The maximum difference in total occupancy between two sequences to attempt matching.")
                 .hasArg()
-                .argName("maximum")
+                .argName("number")
                 .build();
         matchCDR3options.addOption(graphFilename);
         matchCDR3options.addOption(minOccupancyOverlap);