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-rw-r--r--bh20sequploader/qc_fasta.py2
1 files changed, 1 insertions, 1 deletions
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)