Collapse variability for a set of genes across samples.
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This program provides consensus sequences for the genes within a contigs-db and profile-db pair.
In other words, this collapses variability by assigning the most abundant nucleotide in your sample at each position, giving single consensus sequences for each gene for each sample.
A basic run of this program will resemble the following:
anvi-gen-gene-consensus-seuqences -p profile-db \ -c contigs-db \ -o genes-fasta
The default output is a genes-fasta, but you can also get a tab-delimited output matrix by adding the flag
You also have the option to focus on a subset of the data in your contigs-db and profile-db by providing either:
--conpress samples. This way, the program will only report one consensus sequence for each gene instead of reporting one for each sample.
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.