oligotag: Designs a set of oligonucleotides with specified properties

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

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