Scroll to navigation

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

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.



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.



Minimal size of the oligonucleotide family to be generated.

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

Maximum number of G or C in the oligonucleotides.

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


CAUTION:

pattern length must have the same length as oligonucleotides.



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


CAUTION:

pattern length must have the same length as oligonucleotides.



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

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

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

COMMON OPTIONS

Shows this help message and exits.

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

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