Microbial 'omics


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anvi-gen-gene-consensus-sequences [program]

Collapse variability for a set of genes across samples.

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

Table of Contents

Can provide

genes-fasta

Can consume

profile-db contigs-db

Usage

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 --tab-delimited.

You also have the option to focus on a subset of the data in your contigs-db and profile-db by providing either:

  • 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)

Additional Parameters

  • 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 --contigs-mode
  • To report all consensus sequences (even when there are no variable positions), activate --quince-mode

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.