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

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Can consume


Can provide



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:

anvi-oligotype-linkmers -i linkmers-txt

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.

Additional Resources

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.