single-profile-db
Table of Contents
A DB-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..
🔙 To the main page of anvi’o programs and artifacts.
Provided by
Required or used by
anvi-import-taxonomy-for-layers anvi-interactive anvi-merge anvi-summarize-blitz
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.
- You can only run anvi-report-inversions using single profile database created with the inversion fetch filter.
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.