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OLIGOTAG(1) OBITools OLIGOTAG(1)

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
January 28, 2019 1.02 12