From d63263b530d2ef95bdf2efcd1594c52dfa248d1c Mon Sep 17 00:00:00 2001
From: nicolas-zimmermann <nicolaszimmermann.snv@gmail.com>
Date: Thu, 24 Oct 2019 15:00:44 +0200
Subject: [PATCH] added question 3 and 4

---
 wgs.sh | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/wgs.sh b/wgs.sh
index 177fa76..be9ba9c 100644
--- a/wgs.sh
+++ b/wgs.sh
@@ -24,3 +24,8 @@ grep ">" databases/all_genome.fasta|cut -f 2 -d ">" > results/association.tsv
 
 # Question 3
 
+soft/megahit --k-list 21 --mem-flag 0 -1 EchE_R1.fastq.gz -2 EchE_R2.fastq.gz -o contigs
+
+# Question 4
+
+soft/prodigal -i contigs/final.contigs.fa -f fasta > genes.fna