Microbial 'omics


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Table of Contents

CONCEPT

A CONCEPT-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..

Back to the main page of anvi’o programs and artifacts.

Provided by

anvi-profile

Required or used by

anvi-gen-variability-profile

Description

In the context of anvi’o, variability means divergence of environmental populations from the reference used to perform metagenomic read recruitment.

Here, the term “population” describes an assemblage of co-existing microbial genomes in an environment that are similar enough to map to the context of the same reference genome.

Variability profile of a metagenome enables studies of microbial population genetics with anvi’o.

There are two types of variability the program anvi-profile can characterize and store: substitutions, and indels.

Substitutions: SNVs, SCVs, SAAVs

Anvi’o can make sense of single-nucleotide variants (SNVs), single-codon variants (SCVs), and single-amino acid variants (SAAVs). See [this article]((http://merenlab.org/2015/07/20/analyzing-variability).

You can learn the name of the table in which anvi’o stores in a given profile-db by running this command in your anvi’o environment:

python -c 'import anvio.tables as t; print(t.variable_nts_table_name)'

This will tell you about its structure:

python -c 'import anvio.tables as t; print(t.variable_nts_table_structure)'

Indels: insertions and deletions

Anvi’o can also characterize insertions and deletions found within an environment based on short-read recruitment results and will store in the following table:

python -c 'import anvio.tables as t; print(t.indels_table_name)'

Notes for programmers: The convention for the start position of an insertion is defined like so:

    pos_in_contig ...0123456 7890123456
    reference     ...CTACTAC TACTTCATGA...
    read              TACTAC TAC
    insertion               └──ACTG

In this case, the start position of the insertion in the contig is 6. The insertion follows the position it is defined by. This is opposite to IGV, in which the insertion precedes the position it is defined by.

For deletions, there is no such ambiguity in the start position, since the deletion starts on a reference position, not in between two reference positions.

Edit this file to update this information.