Collapse variability for a set of genes across samples.
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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:
The default output is a genes-fasta, but you can also get a tab-delimited output matrix by adding the flag
- A list of gene caller IDs (either as a parameter or through a file with one gene caller ID put line)
- A list of samples to focus on (as a file with a single sample name per line)
- You have the option to change the variability engine (i.e. to codons), where variability at this level will be resolved.
- To compress all variability profiles for each of your samples for a single gene, use the flag
--conpress samples. This way, the program will only report one consensus sequence for each gene instead of reporting one for each sample.
- You can get consensus sequences for each contig instead of for each gene with
- To report all consensus sequences (even when there are no variable positions), activate
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.