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