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