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review method for guessing technology #145

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iqbal-lab opened this issue Jan 18, 2022 · 0 comments

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iqbal-lab commented Jan 18, 2022

see comment here

mykrobe/src/mykrobe/cmds/amr.py

Lines 340 to 342 in b4a19c2

    
           if args.guess_sequence_method and kmer_count_error_rate > 0.001: 
        
               logger.warning("Guess sequence method is on, and we've guessed ONT") 
        
               args.ont = True

Currently we estimate error rate and guess tech from that - I dont know why we dont use read length instead

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