---
name: "oligotag"
section: "1"
platform: "linux"
package: "obitools"
version: "1.2.12+dfsg-2"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/oligotag"
---

# oligotag(1)

description of oligotag oligotag designs a set of oligonucleotides that can be used for tagging a set of samples during PCR reactions, by adding the oligonucleotides on the 5’ end of the primers. Many options allow designing a set of oligonucleotides according to specified properties.

## NAME

oligotag - description of oligotag

*oligotag* designs a set of oligonucleotides that can be used for tagging a set  of samples during PCR reactions, by adding the oligonucleotides on the 5’ end of the primers. Many options allow designing a set of oligonucleotides according to specified properties.

## OLIGOTAG SPECIFIC OPTIONS

- **-L \<filename\>, --oligo-list=\<filename\>**

  Filename containing a list of oligonucleotides. *oligotag* selects within this list the oligonucleotides that match the specified options.

  **CAUTION:**

  Cannot be used with the **-s** option.

- **-s ###, --oligo-size=###**

  Size of oligonucleotides to be generated.

  **CAUTION:**

  Cannot be used with the **-L** option.

  **WARNING:**

  A size equal or greater than eight often leads to a very long computing time and requires a large amount of memory.

- **-f ###, --family-size=###**

  Minimal size of the oligonucleotide family to be generated.

- **-d ###, --distance=###**

  Minimal Hamming distance (number of differences) between two oligonucleotides.

- **-g ###, --gc-max=###**

  Maximum number of G or C in the oligonucleotides.

- **-a \<IUPAC\_PATTERN\>, --accepted=\<IUPAC\_PATTERN\>**

  Selected oligonucleotides are constrained by the given pattern (only IUPAC symbols are allowed).

  **CAUTION:**

  pattern length must have the same length as oligonucleotides.

- **-r \<IUPAC\_PATTERN\>, --rejected=\<IUPAC\_PATTERN\>**

  Selected oligonucleotides do not match the given pattern (only IUPAC symbols are allowed).

  **CAUTION:**

  pattern length must have the same length as oligonucleotides.

- **-p ###, --homopolymer=###**

  Selected oligonucleotides do not contain any homopolymer longer than the specified length.

- **-P ###, --homopolymer-min=###**

  Selected oligonucleotides contain at least one homopolymer longer or equal to the specified length.

- **-T \<seconde\>, --timeout=\<seconde\>**

  Timeout to identify a set of oligonucleotides of required size, as defined by the **-f** option.

## COMMON OPTIONS

- **-h, --help**

  Shows this help message and exits.

- **--DEBUG**

  Sets logging in debug mode.

## EXAMPLES

*Example 1:*

```
> oligotag -s 5 -f 24 -d 3 -g 3 -p 2 > mytags.txt
```

Searches for a family of at least 24 oligonucleotides of a length of 5 nucleotides, with at least 3 differences among them, with a maximum of 3 C/G, and without homopolymers longer than 2. The resulting list of oligonucleotides is saved in the **mytags.txt** file.

*Example 2:*

```
>  oligotag -d 5 -L my_oligos.txt -f 10 -p 1
```

Searches for a subset of at least 10 oligonucleotides listed in the **my\_oligos.txt** file, with at least 5 differences among them, and without homopolymers. The **my\_oligos.txt** file must contain a set of oligonucleotides of the same length, with only one oligonucleotide per line. The resulting list of oligonucleotides is printed on the terminal window.

*Example 3:*

```
> oligotag -s 7 -f 96 -d 3 -p 1 -r cnnnnnn > mytags.txt
```

Searches for a family of at least 96 oligonucleotides of a length of 7 nucleotides, with at least 3 differences among them, without homopolymers, and without a **C** in the first position. The resulting list is saved in the **mytags.txt** file.

*Example 4:*

```
> oligotag -s 9 -f 24 -d 3 -a yryryryry > mytags.txt
```

Searches for a family of at least 24 oligonucleotides of a length of 9 nucleotides, with at least 3 differences among them, and an alternation of pyrimidines and purines. The resulting list is saved in the **mytags.txt** file. Because of the constraints imposed by the **-a** option, it is possible to compute longer oligonucleotides in a reasonable time.

## REFERENCE

- E.

  Coissac. Oligotag: a program for designing sets of tags for next-generation sequencing of multiplexed samples. Methods Mol Biol, 888:13-31, 2012.

## AUTHOR

The OBITools Development Team - LECA

## COPYRIGHT

2019 - 2015, OBITool Development Team