---
name: "dnapi.py"
section: "1"
platform: "linux"
package: "dnapi"
version: "1.1-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/dnapi.py"
---

# dnapi.py(1)

Predict or evaluate 3'adapter sequence(s)

## 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.