Microbial 'omics

Brought to you by

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).

See program help menu or go back to the main page of anvi’o programs and artifacts.

Table of Contents



Requires or uses



Converting a FASTA file to a contigs FASTA

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 short reads from FASTA

Removing short contigs from a FASTA file will improve the performance of the contigs-db later. Running the same command this way will also remove 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.