Update README.md

Usage updated

Author: jontaklee

README.md

@@ -4,8 +4,8 @@ a computational pipeline for typing the Borrelia OspA protein
 ## Installation
 Clone the repository and enter the directory:
 
-    git clone https://github.com/Pfizer-rd/Lyme-In-Silico-Typing-Tool.git
-    cd Lyme-In-Silico-Typing-Tool
+    git clone https://github.com/Pfizer-opensource/LISTT.git
+    cd LISTT
 
 Build and activate the environment:
 
@@ -16,9 +16,11 @@ Build and activate the environment:
 
 LISTT takes an assembled _Borrelia_ genome or Illumina NGS reads of the _ospA_ gene as input:
 
-    python ospa_typing.py -r1 [read1 fastq] -r2 [read2 fastq] -p [path to fastq files] -m r
+    python ospa_typing.py -r1 [read1 fastq] -r2 [read2 fastq] -m r
 
-    python ospa_typing.py -g [genome fasta] -p [path to genome] -m a
+    python ospa_typing.py -g [genome fasta] -m a
+
+Users may also specify the input file(s) location [-p] if an absolute path is not provided.
 
 Analysis will fail if there is insufficient coverage of _ospA_ or if _ospA_ is truncated in the genome assembly.