---
name: "MaskPrimers.py"
section: "1"
platform: "linux"
package: "presto"
version: "0.7.2-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/MaskPrimers.py"
---

# MaskPrimers.py(1)

Removes primers and annotates sequences with primer and barcode identifiers

## NAME

MaskPrimers.py - Removes primers and annotates sequences with primer and barcode identifiers

## DESCRIPTION

usage: MaskPrimers.py \[--version\] \[-h\]  ...

Removes primers and annotates sequences with primer and barcode identifiers

### help:

- **--version**

  show program's version number and exit

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

  show this help message and exit

### subcommands:

-

  Alignment method

- align

  Find primer matches using pairwise local alignment.

- score

  Find primer matches by scoring primers at a fixed position.

- extract

  Remove and annotate a fixed sequence region.

### output files:

-

  mask-pass

-

  processed reads with successful primer matches.

-

  mask-fail

-

  raw reads failing primer identification.

### output annotation fields:

-

  SEQORIENT

-

  the orientation of the output sequence. Either F (input) or RC (reverse complement of input).

-

  PRIMER

-

  name of the best primer match.

-

  BARCODE

-

  the sequence preceding the primer match. Only output when the **--barcode** flag is specified.

## AUTHOR

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