dnapi.py - Predict or evaluate 3'adapter sequence(s)

        This manpage was written by Andreas Tille for the Debian distribution and
        can be used for any other usage of the program.

dnapi.py 1.1                                       March 2020                                        DNAPI.PY(1)

       usage: dnapi.py [options] FASTQ

       Predict or evaluate 3'adapter sequence(s)

   positionalarguments:
       FASTQ  including stdin or compressed file {zip,gz,tar,bz}

   optionalarguments:-h, --help
              show this help message and exit

       --version
              show program's version number and exit

   adapterpredictionparameters:-k [KMER_BEG:KMER_END:INCREMENT | KMER_LEN]
              range of kmers or a single kmer to predict 3'adapters (default: 9:11:2)

       -r [RATIO_BEG:RATIO_END:INTCREMENT | RATIO]
              range of ratios or a single ratio to filter less abundant kmers (default: 1.2:1.4:0.1)

       --show-all
              show other candidates if any

   exhaustiveadaptersearch:--map-command COMMAND
              read mapping command to be tested

       --subsample-rate FLOAT
              subsampling fraction of reads (default: 1.0)

       --output-dir DIRECTORY
              output directory to write report and cleansed reads (default: ./dnapi_out)

       --no-output-files
              only display report and suppress output files

       --temp-dir DIRECTORY
              place to make temporary directory (default: /tmp)

   evaluationofcandidateadapters:--adapter-seq SEQ [SEQ ...]
              list of 3'adapters for evaluation

   adapterremovalparameters:--prefix-match LENGTH
              3'adapter match length to trim (default: 7)

       --min-len LENGTH
              minimum read length to keep for mapping (default: 16)

       --max-len LENGTH
              maximum read length to keep for mapping (default: 36)

       --trim-5p LENGTH
              trim specified number of bases from 5'ends after adapter removal (default: 0)

       --trim-3p LENGTH
              trim specified number of bases from 3'ends after adapter removal (default: 0)

       Report bug to: Junko Tsuji <jnktsj@gmail.com>

       dnapi.py - Predict or evaluate 3'adapter sequence(s)