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.

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.