readme

README.rst

@@ -9,24 +9,39 @@ The Je tool suite
 
 Contains
 ++++++++
-Je currently offers 4 tools :
-
+Je currently offers the following tools :
+
+  **je debarcode** 
+     
+     demultiplexs multi-samples fastq files using user-defined input *read-layouts* and write output files following user-defined *output-layouts*.
+     Replaces both **demultiplex-illu** and **demultiplex** since version 2.0.
+  
+  **je dropseq**
+     
+     to process drop-seq results: clips cell barcode and UMI from read 1 and adds them to header of read 2 (a unique output fastq is created).
+  
+  **je retag**
+  
+    extracts barcode(s) and UMI sequence(s) embedded in read names of a BAM file and migrate them to proper BAM tags.
+  
   **je clip**
 
-    to remove UMIs contained in reads of fastq files that do not need sample demultiplexing
+    removes UMIs contained in reads of fastq files that do not need sample demultiplexing
+    
+  **je markdupes**
+
+     filters BAM files for read duplicates taking UMIs into account.
 
   **je demultiplex**
 
-    to demultiplex multi-samples fastq files which reads contain barcodes and UMIs (or not)
+    to demultiplex multi-samples fastq files which reads contain barcodes and UMIs (or not). Deprecated since version 2.0 (use *je debarcode* instead). 
 
   **je demultiplex-illu**
 
      to demultiplex fastq files according to associated index files (contain the sample encoding barcodes).
-     Reads can additionally contain UMIs (inline)
-
-  **je markdupes**
+     Reads can additionally contain UMIs (inline). Deprecated since version 2.0 (use *je debarcode* instead).
 
-     to filter BAM files for read duplicates taking UMIs into account
+  
 
 
 Distributions
@@ -38,7 +53,7 @@ Source
 ++++++
 
 src/shell/je
-    is the wrapper script to call ``java -jar je_1.0_bundle.jar``
+    is the wrapper script to call ``java -jar je_*_bundle.jar``
 
 src/galaxy/
     contains the Je wrappers for Galaxy