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

# to\_fasta.py(1)

Remove adapters and collapse reads from FASTQ to FASTA

## NAME

to\_fasta.py - Remove adapters and collapse reads from FASTQ to FASTA

## DESCRIPTION

usage: to\_fasta.py \[-h\] \[-3 SEQ\] \[-5 SEQ\] \[--trim-5p BP\] \[--trim-3p BP\]

-

  \[--seed-5p BP\] \[--seed-3p BP\] \[-m BP\] \[-x BP\] \[-s\] \[-B\] \[-a\] FASTQ

Remove adapters and collapse reads from FASTQ to FASTA

### positional arguments:

- FASTQ

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

### optional arguments:

- **-h**, **--help**

  show this help message and exit

- **-3** SEQ

  3'adapter sequence

- **-5** SEQ

  5'adapter sequence

- **--trim-5p** BP

  trim specified number of bases from 5'ends

- **--trim-3p** BP

  trim specified number of bases from 3'ends

- **--seed-5p** BP

  5' adapter match length in bp (default: 7)

- **--seed-3p** BP

  3' adapter match length in bp (default: 7)

- **-m** BP

  minimum read length in bp (default: 16)

- **-x** BP

  maximum read length in bp (default: 36)

- **-s**

  sensitive adapter search with 1 mismatch (default: off)

- **-B**

  only print the reads with both 5' and 3' adapter matches

- **-a**

  print all reads with and without adapter matches if the reads are in the range specified with '-m' and '-x'

## AUTHOR

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