From cf035bd6c5da3f08bf0c7bb78a37173986f86847 Mon Sep 17 00:00:00 2001
From: ACCakut <7684542+ACCakut@users.noreply.github.com>
Date: Wed, 3 May 2023 11:27:47 +0200
Subject: [PATCH] Added software sources

---
 0_WGSPipeline/README.md | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/0_WGSPipeline/README.md b/0_WGSPipeline/README.md
index 141a78f..8b3471f 100644
--- a/0_WGSPipeline/README.md
+++ b/0_WGSPipeline/README.md
@@ -1,11 +1,21 @@
 # About the scripts in this folder:
 
 - **0_DicIndex.sh**
-  - The dictionaries needed for the alignment steps are indexed and sorted.  
+  - The dictionaries needed for the alignment steps are indexed and sorted.
+  - Programs used in the script
+      - BWA https://github.com/lh3/bwa
+      - samfold from https://github.com/samtools/samtools
+      - Picard https://github.com/broadinstitute/picard (requires Java)
 
 - **1_QCScript.sh**
   - Raw reads are trimmed and adapters are removed. The read quality is assessed before and after the trimming.
+  - Programs used in the script
+      - FastQC https://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqc
+      - Trimmomatic https://github.com/usadellab/Trimmomatic
 
 - **2_CombiScriptSamtools.sh**
-  - The trimmed reads are aligned to the reference and variants are called. The coverage at each position is evaluated. 
-
+  - The trimmed reads are aligned to the reference and variants are called. The coverage at each position is evaluated.
+  - Programs used in the script
+      - bwa and samtools, see above
+      - BCFtools https://github.com/samtools/bcftools
+      - Bedtools 2 https://github.com/arq5x/bedtools2