fasta-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

anvi-script-gen-fasta-txt

Required by

anvi-reorient-genomes

Description

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

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

You can also add a structure_genes_of_interest column, which points to a genes-of-interest-txt for each FASTA file. When structure prediction is turned on in the contigs workflow, anvi’o predicts structures only for these genes, and for every gene of a FASTA file that has no value in this column (see the contigs workflow for details).

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

Edit this file to update this information.