Microbial 'omics

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fasta-txt [artifact]

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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.

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

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 or used by



This is a file used by anvi-run-workflow that lists the name and path of all of the input fasta files.

As of now, this file is used in the contigs-workflow, pangenomics-workflow, and the reference mode of the metagenomics-workflow.

In its simplest form, a fasta-txt is a TAB-delmited file with two columns for name and path. Here is an example:

name path
SAMPLE_01 path/to/sample_01.fa
SAMPLE_02 path/to/sample_02.fa

Paths can be absolute or relative, and FASTA files can be compressed or not. That’s all up to you.

One of the primary users of the fasta-txt is the anvi’o snakemake workflows, and to make it more compatible to complex workflow needs, fasta-txt supports the following additional columns to provide more information for each FASTA file when available, such as external-gene-calls file and/or a functions-txt.

Here is an example with those additional columns:

name path external_gene_calls gene_functional_annotation
SAMPLE_01 path/to/sample_01.fa external-gene-calls_01.txt functions-txt_01.txt
SAMPLE_02 path/to/sample_02.fa external-gene-calls_02.txt functions-txt_02.txt

For more information, check out the anvi’o workflow tutorial

Edit this file to update this information.