contigs-fasta [artifact]

A FASTA-type anvi’o artifact. This artifact can be generated, used, and/or exported by anvi’o. It can also be provided by the user for anvi’o to import into its databases, process, and/or use.

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Provided by

anvi-export-contigs anvi-export-splits-and-coverages anvi-script-filter-fasta-by-blast anvi-script-process-genbank anvi-script-process-genbank-metadata anvi-script-reformat-fasta

Required or used by

anvi-gen-contigs-database anvi-script-filter-fasta-by-blast

Description

A contigs-fasta is a fasta file that is suitable to be used by anvi-gen-contigs-database to create a contigs-db.

The most critical requirement for this file is that it must have simple deflines. If your fasta file doesn’t have simple deflines, it is not a proper contigs-fasta. If you intend to use this file with anvi’o, you must fix your FASTA file prior to mapping.

Take a look at your deflines prior to mapping, and remove anything that is not a digit, an ASCII letter, an underscore, or a dash character. Here are some example deflines that are not suitable for a fasta to be considered a contigs-fasta

>Contig-123 length:4567 
>Another defline 42
>gi|478446819|gb|JN117275.2|

And here are some OK ones:

>Contig-123
>Another_defline_42
>gi_478446819_gb_JN117275_2

The program anvi-script-reformat-fasta can do this automatically for you.

Edit this file to update this information.