contig-classification-txt

A TXT-type anvi’o artifact. This artifact is typically provided by the user for anvi’o to import into its databases, process, and/or use.

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Provided by

There are no anvi’o tools that generate this artifact, which means it is most likely provided to the anvi’o ecosystem by the user.

Required by

anvi-import-contig-classification

Description

A tab-delimited file describing the classification of contigs in a contigs-db. This file is the input to anvi-import-contig-classification.

You can create this file based on the output from whichever software you used to classify your contigs (or based on your own classification strategy). Different tools produce different output formats and often use different names for domain-level classes; hence, for consistency, it is up to you to wrangle those outputs so that they fit into the standardized set of classes that anvi’o knows about (as described in contig-classification).

The file must contain the following columns:

Column	Type	Description
contig	text	Contig name (must match a contig in the contigs database)
class	integer	Standardized class: 0=non-eukaryotic, 1=eukaryotic, 2=virus, 3=plasmid, 4=organelle, 5=unclassified
source	text	Name of the tool that produced the classification (e.g. genomad, tiara, custom)
tool_classification	text	Raw classification string from the tool; use semicolons for multi-level entries (e.g. Viruses;Duplodnaviria;Heunggongvirae)
confidence	text	Confidence score from the tool, or NA if not available

A few important notes:

• all contig names must match contigs in the target contigs-db
• a single file may contain classifications from multiple tools (multiple source values)
• only the class column is used downstream (i.e., by anvi-split), while the tool_classification column is just for you to be able to remember the original classification assignment coming from whichever tool(s) you used. It’s therefore important for you to make sure the class column accurately reflects the original classification (note that anvi’o cannot automatically sanity check this for you, because the classifications from different software can be vastly different in format)

Here is an example file:

contig	class	source	tool_classification	confidence
Day17a_QCcontig1	0	genomad	Bacteria;Firmicutes	0.95
Day17a_QCcontig33	0	genomad	Bacteria;Firmicutes	0.92
Day17a_QCcontig4	0	genomad	Bacteria;Proteobacteria	0.88
Day17a_QCcontig74	0	genomad	Bacteria;Bacteroidetes	0.91
Day17a_QCcontig6	1	tiara	eukaryote	NA
Day17a_QCcontig86	0	tiara	bacteria	NA
Day17a_QCcontig90	0	tiara	bacteria	NA
Day17a_QCcontig205	2	tiara	virus	NA

The standardized classes aren’t enough for you? Let us know by opening an issue in the anvi’o Github repository.

Edit this file to update this information.