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Diffstat (limited to 'bh20sequploader/qc_fasta.py')
| -rw-r--r-- | bh20sequploader/qc_fasta.py | 2 |
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) |