final renaming

1 files changed, 16 insertions, 15 deletions

diff --git a/README.md b/README.md
index 18c0748..7642341 100644
--- a/README.md
+++ b/README.md
@@ -15,7 +15,7 @@ PI: http://brisson.bio.upenn.edu/
 * [Requirements](#requirements)
 * [Setup](#setup)
 * [Example Usage](#example-usage)
-  * [SGA User Interface](#sga-user-interface)
+  * [SWGA User Interface](#sga-user-interface)
   * [Setting Tunable Parameters](#setting-tunable-parameters)
   * [Running Individual Steps](#running-individual-steps)
   * [Manually Scoring Specific Mer Combinations From List ](#manually-scoring-specific-mer-combinations-from-list)
@@ -42,23 +42,24 @@ To use this you'll need:
  
 ## Setup
 
-    git clone git@github.com:mutantturkey/SelectiveWholeGenomeAmplification".git
-    cd SelectiveWholeGenomeAmplification"
+    git clone git@github.com:mutantturkey/SelectiveWholeGenomeAmplification.git
+    cd SelectiveWholeGenomeAmplification
     make
     sudo make install
 
 ## Example Usage
-Standard use of (SGA) SelectiveWholeGenomeAmplification" is easy. it takes two arguments,
+Standard use of (SGA) SelectiveWholeGenomeAmplification is easy. it takes two arguments,
 the foreground and background
 
 
-    SelectiveWholeGenomeAmplification" PfalciparumGenome.fasta HumanGenome.fasta;
+    SelectiveWholeGenomeAmplification PfalciparumGenome.fasta HumanGenome.fasta;
     less PfalciparumGenome_HumanGenome/final_mers
 
-### SGA User Interface
-SGA also comes with a easy to use user prompt called SelectiveWholeGenomeAmplification"UI.
-It allows for a less experienced user to use
-SGA without issue. to run this all you need to do is run SelectiveGenomeAmiplifcationUI and you'll see a series of prompts asking the user about tunables like below
+### SWGA User Interface
+SWGA also comes with a easy to use user prompt called SelectiveWholeGenomeAmplificationUI.
+It allows for a less experienced user to use SWGA without issue. to run this
+all you need to do is run SelectiveGenomeAmiplifcationUI and you'll see a
+series of prompts asking the user about tunables like below
 
     Where would you like to temporary files to be stored? (Default=$output_directory/.tmp): 
     Where would you like to count files to be stored? (Default=$output_directory/.tmp): 
@@ -69,7 +70,7 @@ SGA without issue. to run this all you need to do is run SelectiveGenomeAmiplifc
     Input the path to your foreground file:target.fa  
     Input the path to your background file:humangenome.fa 
     Would you like to output your inserted variables to a string you can later paste? (Y/N/Default=y): n
-    Run SelectiveWholeGenomeAmplification"? (Y/N/Default=y): y
+    Run SelectiveWholeGenomeAmplification? (Y/N/Default=y): y
 
 ### Setting Tunable Parameters
 
@@ -78,19 +79,19 @@ below.  For user customizable variables, they need to be passed in as
 environmental variables like so:
 
     max_mer_distance=5000 max_select=6 min_mer_range=6 max_mer_range=12 \
-    SelectiveWholeGenomeAmplification".sh PfalciparumGenome.fasta half.fasta 
+    SelectiveWholeGenomeAmplification.sh PfalciparumGenome.fasta half.fasta 
 
 
 ### Running individual steps
 
-By default SelectiveWholeGenomeAmplification" runs all four steps, but you can
+By default SelectiveWholeGenomeAmplification runs all four steps, but you can
 specify the program to run other steps, like in these examples.
 
-    current_run=run_1 SelectiveWholeGenomeAmplification" target.fasta bg.fasta score
+    current_run=run_1 SelectiveWholeGenomeAmplification target.fasta bg.fasta score
 
-    current_run=run_1 SelectiveWholeGenomeAmplification" target.fasta bg.fasta select score
+    current_run=run_1 SelectiveWholeGenomeAmplification target.fasta bg.fasta select score
 
-    current_run=run_1 SelectiveWholeGenomeAmplification" target.fasta bg.fasta 3 4 
+    current_run=run_1 SelectiveWholeGenomeAmplification target.fasta bg.fasta 3 4 
 
 valid steps are these: