fasta [artifact]

A FASTA-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-dereplicate-genomes anvi-script-fix-homopolymer-indels

Required or used by

anvi-dereplicate-genomes anvi-script-compute-ani-for-fasta anvi-script-fix-homopolymer-indels anvi-script-reformat-fasta

Description

A FASTA-formatted file that does not necessarily meet the standards of a contigs-fasta.

anvi-script-reformat-fasta can turn a regular fasta into a contigs-fasta, which anvi’o will be able to utilize better.

But what is a FASTA file?

A FASTA file contains sequences (in this case, nucleotide sequences, though they can also describe peptide sequences) that are formatted as follows:

>SEQUENCE_ID VARIOUS_SEQUENCE_DATA
SEQUENCE

The VARIOUS_SEQUENCE_DATA region can contain data such as the NCBI taxon ID, GI accession number, a text description of the sequence, or the start and end positions if the sequence is a portion of a larger sample. All of this information is optional.

The sequence itself is written in standard IUPAC format (though it can be written in lower-case letters).

For a concrete example, you can download sequences from the NCBI database in FASTA format.

Edit this file to update this information.