fastfasta

Fastfasta is a software utility and library designed for working with FASTA sequence files in bioinformatics workflows. It aims to provide fast, memory-efficient handling of large sequence collections, enabling common operations without loading entire files into memory.

Key features include streaming parsing of FASTA records, sequence filtering by length or header pattern, GC content evaluation, subsequence extraction, header rewriting, and the ability to split, merge, or concatenate multiple files. It supports random access to records through an index, and it can operate in multi-threaded mode to accelerate CPU-bound tasks. Outputs typically remain in FASTA, but the tool can also generate lightweight summaries or statistics for downstream reporting.

Implementation and availability: fastfasta is distributed as both a command-line program and a library; it provides a stable API and optional bindings for scripting languages to integrate into pipelines. It is cross-platform and released as open-source software, with documentation and example workflows provided in its repository.

Development and ecosystem: The project is maintained by an international contributor base and integrates with common bioinformatics pipelines. It is often used to preprocess large genomes, prepare data for alignment, or generate filtered datasets for downstream analysis.