.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.13.
.TH DNAPI.PY "1" "March 2020" "dnapi.py 1.1" "User Commands"
.SH NAME
dnapi.py \- Predict or evaluate 3'adapter sequence(s)
.SH DESCRIPTION
usage: dnapi.py [options] FASTQ
.PP
Predict or evaluate 3'adapter sequence(s)
.SS "positional arguments:"
.TP
FASTQ
including stdin or compressed file {zip,gz,tar,bz}
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-version\fR
show program's version number and exit
.SS "adapter prediction parameters:"
.TP
\fB\-k\fR [KMER_BEG:KMER_END:INCREMENT | KMER_LEN]
range of kmers or a single kmer to predict 3'adapters
(default: 9:11:2)
.TP
\fB\-r\fR [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)
.TP
\fB\-\-show\-all\fR
show other candidates if any
.SS "exhaustive adapter search:"
.TP
\fB\-\-map\-command\fR COMMAND
read mapping command to be tested
.TP
\fB\-\-subsample\-rate\fR FLOAT
subsampling fraction of reads (default: 1.0)
.TP
\fB\-\-output\-dir\fR DIRECTORY
output directory to write report and cleansed reads
(default: ./dnapi_out)
.TP
\fB\-\-no\-output\-files\fR
only display report and suppress output files
.TP
\fB\-\-temp\-dir\fR DIRECTORY
place to make temporary directory (default: \fI\,/tmp\/\fP)
.SS "evaluation of candidate adapters:"
.TP
\fB\-\-adapter\-seq\fR SEQ [SEQ ...]
list of 3'adapters for evaluation
.SS "adapter removal parameters:"
.TP
\fB\-\-prefix\-match\fR LENGTH
3'adapter match length to trim (default: 7)
.TP
\fB\-\-min\-len\fR LENGTH
minimum read length to keep for mapping (default: 16)
.TP
\fB\-\-max\-len\fR LENGTH
maximum read length to keep for mapping (default: 36)
.TP
\fB\-\-trim\-5p\fR LENGTH
trim specified number of bases from 5'ends after
adapter removal (default: 0)
.TP
\fB\-\-trim\-3p\fR LENGTH
trim specified number of bases from 3'ends after
adapter removal (default: 0)
.PP
Report bug to: Junko Tsuji <jnktsj@gmail.com>
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.