Microbial 'omics


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profile-db [artifact]

Table of Contents

DB

A DB-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-merge

Required or used by

anvi-3dev anvi-cluster-contigs anvi-db-info anvi-delete-collection anvi-delete-misc-data anvi-delete-state anvi-display-metabolism anvi-estimate-genome-completeness anvi-estimate-metabolism anvi-estimate-scg-taxonomy anvi-export-collection anvi-export-gene-coverage-and-detection anvi-export-items-order anvi-export-misc-data anvi-export-splits-and-coverages anvi-export-state anvi-gen-fixation-index-matrix anvi-gen-gene-consensus-sequences anvi-gen-gene-level-stats-databases anvi-gen-variability-profile anvi-get-aa-counts anvi-get-sequences-for-hmm-hits anvi-get-short-reads-from-bam anvi-get-split-coverages anvi-import-collection anvi-import-items-order anvi-import-misc-data anvi-import-state anvi-inspect anvi-interactive anvi-merge-bins anvi-refine anvi-rename-bins anvi-show-collections-and-bins anvi-show-misc-data anvi-split anvi-summarize anvi-update-db-description anvi-script-add-default-collection anvi-script-gen-distribution-of-genes-in-a-bin

Description

An anvi’o database that contains key information about the mapping of short reads from multiple samples to your contigs.

You can think of this as a extension of a contigs-db that contains information about how your contigs align with each of your samples. The vast majority of programs that use a profile database will also ask for the contigs database associated with it.

A profile database contains information about how short reads map to the contigs in a contigs-db. Specificially, for each sample, a profile database contains

  • the coverage and abundance per nucleotide position for each contig
  • variants of various kinds (single-nucleotide, single-codon, and single-amino acid)
  • structural variants (ex. insertions and deletions) These terms are explained on the anvi’o vocabulary page

This information is neccessary to run anvi’o programs like anvi-cluster-contigs, anvi-estimate-metabolism, and anvi-gen-gene-level-stats-databases. You can also interact with a profile database using programs like anvi-interactive.

Technically, “profile-db” refers to a profile database that contains the data from several samples – in other words, the result of running anvi-merge on several single-profile-db. However, since a single-profile-db has a lot of the functionality of a profile-db, it might be easier to think of a profile database as a header referring to both single-profile-dbs and profile-dbs (which can also be called a merged-profile-dbs). For simplicity sake, since most users are dealing with multiple samples, the name was shortened to just profile-db. The following are a list of differences in functionality between a single profile database and a merged profile database:

How to make a profile database

If you have multiple samples

  1. Prepare your contigs-db
  2. Run anvi-profile with an appropriate bam-file. The output of this will give you a single-profile-db. You will need to do this for each of your samples, which have been converted into a bam-file with your short reads.
  3. Run anvi-merge on your contigs-db (from step 1) and your single-profile-dbs (from step 2). The output of this is a profile-db.

If you have a single sample

  1. Prepare your contigs-db
  2. Run anvi-profile with an appropriate bam-file. The output of this will give you a single-profile-db. You can see that page for more information, but essentially you can use a single-profile-db instead of a profile database to run most anvi’o functions.

Edit this file to update this information.