Commit 9a597125 authored by Rayan  CHIKHI's avatar Rayan CHIKHI
Browse files

bcalm tweaks

parent 89c7bfc5
......@@ -32,7 +32,7 @@ def process_file(inputBucket, fileName, region, delete_original=False):
print("downloaded file to",local_file)
# run bcalm
os.system(' '.join(["./bcalm","-kmer-size","21","-in",local_file]))
os.system(' '.join(["./bcalm", "-kmer-size", "31", "-in", local_file, "-skip-links"]))
unitigs_filename = '.'.join(local_file.split('.')[:-1])+".unitigs.fa"
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