From 9406e8a025219d7e65df1785070b55ff1a1a86ec Mon Sep 17 00:00:00 2001
From: root <root@EB10PA4.newcefe.newage.fr>
Date: Fri, 6 Dec 2019 21:18:30 +0100
Subject: [PATCH] update optimal pipeline
---
optimal_pipeline/optimal_pipeline.sh | 2 --
1 file changed, 2 deletions(-)
diff --git a/optimal_pipeline/optimal_pipeline.sh b/optimal_pipeline/optimal_pipeline.sh
index 4b398e9..0aae3bb 100644
--- a/optimal_pipeline/optimal_pipeline.sh
+++ b/optimal_pipeline/optimal_pipeline.sh
@@ -64,8 +64,6 @@ $cutadapt --pair-adapters --pair-filter=both -g assigned=^ACACCGCCCGTCACTCT -G a
##Format file post cutadapt for obitools
$obiannotate $main_dir/R1.assigned2.fastq -k sample > $main_dir/R1.assigned3.fastq
$obiannotate $main_dir/R2.assigned2.fastq -k sample > $main_dir/R2.assigned3.fastq
-sed -i -e "s/ sample/_sample/g" $main_dir/R1.assigned3.fastq
-sed -i -e "s/ sample/_sample/g" $main_dir/R2.assigned3.fastq
## forward and reverse reads assembly
assembly=${main_dir}"/"${pref}".fasta"
--
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