Designing edit metric tags

You can design sequence tags of arbitrary length by invoking design_edit_metric_tags.py using something similar to the following:

design_edit_metric_tags.py \
    --tag-length=6 \
    --edit-distance=3 \
    --no-polybase \
    --gc \
    --comp \
    --min-and-greater

We describe each option (design_edit_metric_tags.py --help) in detail, below. We have separated these options into those pertinent to Tag design options and those for Tag rescanning options.

Tag design options

--output=<FILE>
	Path to the output file, in which to store the results of a particular run. When not provided, results are written to stdout.
--tag-length=<int>
	Length of the desired sequence tag. The results output depend on the interaction of –tag-length and –edit-distance: you cannot design tags of greater edit distance than their tag-length - 1. By default, there is always only one tag in the set where –edit-distance = –tag-length.
--edit-distance=<int>
	Edit distance of the desired tag set.
--multiprocessing
	Use multiple processors. The number of cores/processors used is set by default to the max(cores) - 2. You can explicitly set this option using –processors.
--processors=<int>
	The number of computing cores/processors to use. This defaults to max(cores) - 2.
--no-polybase
	Filter those tags having greater than two adjacent, identical bases. Homopolymer bases are problematic on certain sequencing platforms, thus it is useful to avoid homopolymer runs longer than three.
--gc
	Filter those tags having 40 < GC % < 60.
--comp
	Filter those tags that are perfect self-complements. Generally, this option removes tags likely to form hairpins.
--hamming
	Use Hamming distance in place of edit (Levenshtein) distance.
--min-and-greater
	Return all tags at the minimum edit distance requested, and subsets of those tags falling within consecutively greater edit distance categories. Thus, if you design 8 nucleotide, edit distance 3 tags and pass this option, the program will return all subsets of these tags having edit distances in the set([3,4,5,6,7]).

Tag rescanning options

Tag rescanning is an option that you can use to design nested sets of edit metric sequence tags. “Nested” is likely the wrong word without some context. Essentially the rescanning option allows you to:

1. design a set of tags of --tag-length=<int> and --edit-distance=<int>
2. select the subset of those tags where the first x bases also have a particular edit distance from one another

As an example, we designed a set of 10 nucleotide, edit metric sequence tags of edit distance five. Then we selected the subset of these 10 nucleotide tags where the first six nucleotides where also edit distance three from one another.

This allows us an additional layer of protection, in case the index sequencing step on certain platforms is not run for sufficiently long (and only gathers data from the first six bases of the index instead of all 10). You can rescan a sequence tag file, outputting those tags where the first six nucleotides are edit distance three from one another using:

python design_edit_metric_tags.py \
    --rescan my_file_to_rescan.txt \
    --edit-distance=3 \
    --min-and-greater \
    --rescan-length=6

--rescan=<FILE>
	Path to the input file, containing edit metric sequence tags, that you wish you rescan.
--rescan-length=<int>
	The (subset) number of nucleotides over which you wish to determine the nested edit distance.