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authorAndreaGuarracino2020-10-01 22:44:53 +0200
committerAndreaGuarracino2020-10-01 22:44:53 +0200
commitd60b6c7298e62fdc676e722cdfbaecf144536f2e (patch)
tree8787c5ee25f0b49628a0cfb4e7f80d41b000eef3 /bh20sequploader/qc_fasta.py
parentcc9aff0931aa1579c47c01dfa74022807548b40f (diff)
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sequence divergence to 5% for minimap2 in the FASTA quality control
Diffstat (limited to 'bh20sequploader/qc_fasta.py')
-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)