diff --git a/CHANGELOG.md b/CHANGELOG.md
index 42052941a9ea0031bec279ed55c4f32eca68401d..d83c84e00747cc74bee0409647542c860392be8f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,12 +1,13 @@
 # v3.0.0
 **User Facing**
-* 
+* Add 5GEX-PE, 5GEX-R2, threeprime as library options
 
 **Background**
 
 *Known Bugs*
 * Vizapp does not yet work for Astrocyte
 * Running in CLI: to set --fastq path of file/s needs to be in quotes
+* 2020-A references don't work with with cellranger versions < 4.0.0 (bug)
 
 # v2.2.0
 **User Facing**
diff --git a/README.md b/README.md
index f221d97744a0fb293e8c20d9dab4f8f57523954b..9542a95a3ed7125a8002585c9e7428a97e2a4ecf 100755
--- a/README.md
+++ b/README.md
@@ -96,9 +96,12 @@ To Run:
     * --version (cellranger version) 2.1.1 can only read --kitVersion of two (2)
     * options:
         * *'auto'*
+        * *'3GEX'*
         * *'3GEXv3'*
         * *'3GEXv2'*
         * *'5GEX'*
+        * *'5GEXPE'*
+        * *'5GEXR2'*
     * eg: **--kitVersion '3GEXv3'**
   * **--version**
     * cellranger version
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index 119d8c3a67133993bdebe5ee8816673884d00368..74f1ebf8fe8198bf02b619de8e6e18a9da001d7f 100755
--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -140,9 +140,12 @@ workflow_parameters:
     default: 'auto'
     choices:
       - ['auto', 'Auto Detect']
+      - ['3GEX', '3prime GEX Auto (3prime Gene Expression)']
       - ['3GEXv3', '3prime GEX v3 (3prime Gene Expression)']
       - ['3GEXv2', '3prime GEX v2 (3prime Gene Expression)']
       - ['5GEX', '5prime GEX Auto (5prime Gene Expression)']
+      - ['5GEXPE', '5prime GEX both R1 and R2 used for alignment (5prime Gene Expression)']
+      - ['5GEXR2', '5prime GEX only R2 used for alignment (5prime Gene Expression)']
     required: true
     description: |
       10x single cell gene expression chemistry version (only used in cellranger version 3.x).
diff --git a/workflow/main.nf b/workflow/main.nf
index 532b661c73b0def69e892f45598e401eced5ba26..e9f5afb1e05fa601a4d1f3a533f493ba7df373f0 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -44,7 +44,9 @@ if (params.astrocyte) {
   } else {
     params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-'
   }
-  if (params.kitVersion == "3GEXv1") {
+  if (params.kitVersion == "3GEX") {
+    params.chemistryParam ='threeprime'
+  } else if (params.kitVersion == "3GEXv1") {
     params.chemistryParam ='SC3Pv1'
   } else if (params.kitVersion == "3GEXv2") {
     params.chemistryParam ='SC3Pv2'
@@ -52,6 +54,10 @@ if (params.astrocyte) {
     params.chemistryParam ='SC3Pv3'
   } else if (params.kitVersion == "5GEX") {
     params.chemistryParam ='fiveprime'
+  } else if (params.kitVersion == "5GEXPE") {
+    params.chemistryParam ='SC5P-PE'
+  } else if (params.kitVersion == "5GEXR2") {
+    params.chemistryParam ='SC5P-R2'
   } else {
     params.chemistryParam = 'auto'
   }