Microbial 'omics

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anvi-script-reformat-fasta [program]

Reformat FASTA file (remove contigs based on length, or based on a given list of deflines, and/or generate an output with simpler names).

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Table of Contents



Requires or uses



This program converts a fasta file to a contigs-fasta. In other words, it reformats your FASTA formatted file to meet the conditions required of a contigs-fasta, which is able to be used by other anvi’o programs.

anvi-script-reformat-fasta fasta \ -o contigs-fasta \ --simplify-names

If you use the flag –report-file, it will also create a TAB-delimited file for you to keep track of which defline in the new file corresponds to which defline in the original file.

Removing the short reads

Removing short contigs from a FASTA file will improve the performance of the contigs-db later. The example below runs the same command while also removing sequences that are shorter than 1,000 nts:

anvi-script-reformat-fasta fasta \ -o contigs-fasta \ -l 1000 \ --simplify-names

Edit this file to update this information.

Additional Resources

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.