single-profile-db [artifact]

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-profile

Required or used by

anvi-import-taxonomy-for-layers anvi-interactive anvi-merge

Description

An anvi’o database that contains the same information as a merged profile-db, namely key information about the mapping of short reads in a single sample to your contigs.

You can think of this as a extension of a contigs-db that contains information about how your contigs align with a single one of your individual samples. If you have more than one sample, you’ll probably want to use anvi-merge to merge your databases into a merged profile-db. The vast majority of programs that use a profile database will also ask for the contigs database associated with it.

A single profile database contains information about how the short reads in a single BAM-file (see bam-file) map to the contigs in a contigs-db. Specificially, 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)

Once created, a single profile database is almost interchangable with a profile-db (even though the names can be a little confusing. Think of a single-profile-db as a type of profile-db, since it has only a few differences). The main differences between the two are as follows:

• You cannot run anvi-cluster-contigs or anvi-mcg-classifier on a single profile db, since these two programs look at the alignment data in many samples.
• You can run anvi-import-taxonomy-for-layers on a single profile database but not a merged one.
• You can only run anvi-merge on a single profile database.

If you want to look at the contents of a single profile database, you can do so using anvi-interactive.

Edit this file to update this information.