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nigyta / dfast_core

DDBJ Fast Annotation and Submission Tool
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Added options to enable GeneMarkS2, Diamond, RNAmmer #26

Closed nigyta closed 4 years ago

nigyta commented 4 years ago

As per the pull request #25 and the issue #20, command-line options to enable GeneMarkS2, Diamond, RNAmmer have been added. See FAQ for more details.

  --aligner STR         Aligner to use [ghostx(=default)|blastp|diamond]
  --use_genemarks2 STR  Use GeneMarkS2 to predict CDS instead of MGA. [auto|bact|arch]
  --use_rnammer STR     Use RNAmmer to predict rRNA instead of Barrnap. [bact|arch]

Note that GeneMarkS2, Diamond, RNAmmer are not bundled in the software package. If you want to use them, please install them by yourself.

Thank @AaronRuben for the PR for GeneMarkS2!