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