NAME

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

DESCRIPTION

       usage: dnapi.py [options] FASTQ

       Predict or evaluate 3'adapter sequence(s)

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

   optional arguments:
       -h, --help
              show this help message and exit

       --version
              show program's version number and exit

   adapter prediction parameters:
       -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

   exhaustive adapter search:
       --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)

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

   adapter removal parameters:
       --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>

AUTHOR

        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)