From d60b6c7298e62fdc676e722cdfbaecf144536f2e Mon Sep 17 00:00:00 2001
From: AndreaGuarracino
Date: Thu, 1 Oct 2020 22:44:53 +0200
Subject: sequence divergence to 5% for minimap2 in the FASTA quality control

---
 bh20sequploader/qc_fasta.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py
index 58ca22e..f567f0a 100644
--- a/bh20sequploader/qc_fasta.py
+++ b/bh20sequploader/qc_fasta.py
@@ -66,7 +66,7 @@ def qc_fasta(arg_sequence, check_with_mimimap2=True):
 
                     similarity = 0
                     try:
-                        cmd = ["minimap2", "-c", tmp1.name, tmp2.name]
+                        cmd = ["minimap2", "-c -x asm20", tmp1.name, tmp2.name]
                         logging.info("QC checking similarity to reference")
                         logging.info(" ".join(cmd))
                         result = subprocess.run(cmd, stdout=subprocess.PIPE)
-- 
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