clean-fasta is an open-source command-line utility designed for bioinformatics professionals to clean and filter FASTA sequence files. It removes gaps, filters sequences by length and valid-character ratio, and deduplicates sequence IDs, streamlining preprocessing for genomics and phylogenetics workflows.
clean-fasta sits in PulseGate's CLI tools & terminal category. It focuses on automating the cleaning and filtering of FASTA sequence files for bioinformatics analysis. clean-fasta is an open-source project aimed at bioinformatics researchers and computational biologists. The project is open source (MIT). It runs on the command line.
cmzmasek builds and maintains clean-fasta, and the product first shipped in 2026. The project is developed in the open on GitHub with 2 commits in the last 90 days. Among its 5 catalogued features are gap removal, length filtering, and character ratio filter.
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