From c41fcaccfdbed494e2acf70a9ed385f8b951c122 Mon Sep 17 00:00:00 2001
From: Simone Maestri <simone.maestri@hotmail.it>
Date: Wed, 18 Dec 2019 08:43:45 +0100
Subject: [PATCH] Update Calculate_mapping_rate.sh

---
 Calculate_mapping_rate.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Calculate_mapping_rate.sh b/Calculate_mapping_rate.sh
index aed2085..6e037ee 100644
--- a/Calculate_mapping_rate.sh
+++ b/Calculate_mapping_rate.sh
@@ -20,8 +20,8 @@ READS=$1
 DRAFT_READS=$2
 CONTIG=$3
 
-MINIMAP2=/path/to/minimap2
-SAMTOOLS=/path/to/samtools
+MINIMAP2=minimap2 #specify full path if you want to use a version of the program which is not in your PATH
+SAMTOOLS=samtools #specify full path if you want to use a version of the program which is not in your PATH
 
 wdir=$(realpath $(pwd))
 reads_full=$wdir"/"$READS