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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.
-h, --help Shows this help message and exits. --DEBUG Sets logging in debug mode.
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.
E. Coissac. Oligotag: a program for designing sets of tags for next-generation sequencing of multiplexed samples. Methods Mol Biol, 888:13-31, 2012.
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2019 - 2015, OBITool Development Team 1.02 12 Jan 28, 2019 OLIGOTAG(1)