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>