Microbial 'omics


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fasta-txt [artifact]

Table of Contents

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 or used by

anvi-run-workflow

Description

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.

This file will look something like this:

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

Note that the paths can be either absolute or relative, and the fasta files can be either compressed or not. That’s all up to you.

To input more information, for each file you can also specify an external-gene-calls file and/or a functions-txt. Just provide those with additional columns, as so:

name        path                    external_gene_calls             gene_functional_annotation
SAMPLE_01   path/to/sample_01.fa    <span class="artifact-n">[external-gene-calls](/software/anvio/help/7/artifacts/external-gene-calls)</span>_01.txt  <span class="artifact-n">[functions-txt](/software/anvio/help/7/artifacts/functions-txt)</span>_01.txt
SAMPLE_02   path/to/sample_02.fa    <span class="artifact-n">[external-gene-calls](/software/anvio/help/7/artifacts/external-gene-calls)</span>_02.txt  <span class="artifact-n">[functions-txt](/software/anvio/help/7/artifacts/functions-txt)</span>_02.txt

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

Edit this file to update this information.