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| author | AndreaGuarracino | 2020-10-01 22:44:53 +0200 |
|---|---|---|
| committer | AndreaGuarracino | 2020-10-01 22:44:53 +0200 |
| commit | d60b6c7298e62fdc676e722cdfbaecf144536f2e (patch) | |
| tree | 8787c5ee25f0b49628a0cfb4e7f80d41b000eef3 /bh20sequploader/qc_fasta.py | |
| parent | cc9aff0931aa1579c47c01dfa74022807548b40f (diff) | |
| download | bh20-seq-resource-d60b6c7298e62fdc676e722cdfbaecf144536f2e.tar.gz bh20-seq-resource-d60b6c7298e62fdc676e722cdfbaecf144536f2e.tar.lz bh20-seq-resource-d60b6c7298e62fdc676e722cdfbaecf144536f2e.zip | |
sequence divergence to 5% for minimap2 in the FASTA quality control
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) |