---
name: "seqmagick"
section: "1"
platform: "linux"
package: "seqmagick"
version: "0.8.6-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/seqmagick"
---

# seqmagick(1)

Manipulate sequence files

## NAME

seqmagick - Manipulate sequence files

## SYNOPSIS

usage: seqmagick \[-h\] \[-V\] \[-v\] \[-q\]

-

  help, convert, info, mogrify, primer-trim, quality-filter, extract-ids, backtrans-align ...

## DESCIPTION

Seqmagick is a little utility to expose the file format conversion in BioPython in a convenient way.

## OPTIONS

### positional arguments:

-

  help, convert, info, mogrify, primer-trim, quality-filter, extract-ids, backtrans-align

- help

  Detailed help for actions using help \<action\>

- convert

  Convert between sequence formats

- info

  Info action

- mogrify

  Modify sequence file(s) in place.

- primer-trim

  Find a primer sequence in a gapped alignment, trim to amplicon

- quality-filter

  Filter reads based on quality scores

- extract-ids

  Extract the sequence IDs from a file

- backtrans-align

  Given a protein alignment and unaligned nucleotides, align the nucleotides using the protein alignment. Protein and nucleotide sequence files must contain the same number of sequences, in the same order, with the same IDs.

### optional arguments:

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

  show this help message and exit

- **-V**, **--version**

  Print the version number and exit

- **-v**, **--verbose**

  Be more verbose. Specify **-vv** or **-vvv** for even more

- **-q**, **--quiet**

  Suppress output

## AUTHOR

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