Microbial 'omics

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Takes an anvi'o linkmers report, generates an oligotyping output.

See program help menu or go back to the main page of anvi’o programs and artifacts.

## Usage

This program converts a linkmers-txt artifact into oligotypes data.

A linkmers-txt artifact describes each of your short reads that mapped to specific target nucleotide positions in a reference contig. This program counts the total occurance of each combination in those target positions within each of your samples.

For example, if your linkmers-txt focused on two target positions, and you ran the following:

The output (which by default is called oligotype-counts-001.txt) might look like the following:

key         AG   CA    CG    GA    GG    TA    TG
sample_001  0    320   12    2     0     3     579
sample_002  0    142   2     0     2     10    353
sample_003  3    404   1     1     0     2     610
sample_004  0    209   6     0     1     0     240


Note that combinations with zero reads in every sample are not included.

Edit this file to update this information.

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.