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shenwei356 / kmcp

Accurate metagenomic profiling && Fast large-scale sequence/genome searching
https://bioinf.shenwei.me/kmcp
MIT License
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Automatically disable ambiguous-matches correction for complex communities with thousands of species #13

Open shenwei356 opened 2 years ago

shenwei356 commented 2 years ago

It's optional for now, but it would be better to be switched on automatically to reduce profiling time.

$ kmcp profile  -h
Generate taxonomic profile from search results

Methods:
  3. We also use the two-stage taxonomy assignment algorithm in MegaPath
     to reduce the false positive of ambiguous matches.
     You can also disable this step by the flag --no-amb-corr.
     If the stage 1/4 produces thousands of candidates, you can also use
     the flag --no-amb-corr to reduce analysis time, which has very little
     effect on the results.

Flags:
      --no-amb-corr                       ► Do not correct ambiguous reads. Use this flag to reduce
                                          analysis time if the stage 1/4 produces thousands of candidates.