juicefasta

Juicefasta is a compact, open-source command-line utility designed for manipulating FASTA-format sequence data in bioinformatics workflows. It provides a set of lightweight operations to filter, reformat, and extract sequences from large FASTA files, aiming to integrate smoothly with typical research pipelines.

Core features include streaming I/O to handle very large files without loading them entirely into memory, support for reading and writing gzip-compressed FASTA, and a range of sequence-level operations such as filtering by length or content, renaming or standardizing headers, extracting subsequences by ID or coordinate range, and splitting or merging multiple files. It also offers utilities for simple metadata generation, such as sequence counts and approximate GC content, and for converting line wrapping and header formatting to match common conventions.

Design and implementation notes: Juicefasta emphasizes a simple, stable command-line interface and deterministic behavior across platforms. By operating in streaming mode, it minimizes peak memory usage and supports integration into automated pipelines. The project aims to be interoperable with other standard bioinformatics tools that consume FASTA inputs and outputs.

Availability: Juicefasta is released under an open-source license and maintained in a public repository. Users can typically install it in cross-platform environments and incorporate it into scripts or workflow managers. The project is actively developed, with updates addressing new sequence formats and performance improvements.

Limitations: The tool focuses on common FASTA manipulations and does not provide a graphical interface. For specialized analyses, users may combine juicefasta with other software to perform more complex transformations.