diff README.rst @ 39:a793ffd0cd04 draft

Uploaded

--- a/README.rst	Fri Oct 10 11:28:57 2014 -0400
+++ b/README.rst	Tue Dec 23 11:26:33 2014 -0500
@@ -1,21 +1,35 @@
-Falco Amplicon Analysis Pipeline & Galaxy wrapper
+FALCO Amplicon Analysis Pipeline & Galaxy wrapper
 ========================================
 
-Text
+FALCO variant-caller is part of the Amplicon Analysis Pipeline (AAP).
+
+The typical workflow is as follows:
+* paired-end amplicon sequencing
+* merge pairs by overlapping them
+* map the single read fastq with BWA
+* perform variant calling with FALCO
+* create (html) report of the results
+
+FALCO uses samtools and straight-forward statistics to determine wether a
+potential variant is likely a (technical) artifact or not.
+
+Input / Output
+=======
+
+Input of the caller is a BAM file, output VCF
 
 
 History
 =======
 
-============== ========================================================================
+============== ================================================================
 Date            Changes
--------------- ------------------------------------------------------------------------
-September 2014   * first release in Tool Shed
-July 2014        * first release in Test Tool Shed
-============== ========================================================================
+-------------- ----------------------------------------------------------------
+December 2014    * first release in Test Tool Shed
+============== ================================================================
 
 
 Bug Reports & other questions
 =============================
 
-Issues can be reported via the contact form at
+Issues can be reported via http://www.tgac.nl/