fasta-txt
Table of Contents
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
There are no anvi’o tools that use or require this artifact directly, which means it is most likely an end-product for the user.
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 |
For more information, check out the anvi’o workflow tutorial
Edit this file to update this information.