FUSTA: leveraging FUSE for manipulation of multiFASTA files at scale

MOTIVATION: FASTA files are the de facto standard for sharing, manipulating and storing biological sequences, while concatenated in multiFASTA they tend to be unwieldy for two main reasons: (i) they can become big enough that their manipulation with standard text-editing tools is unpractical, either due to slowness or memory consumption; (ii) by mixing metadata (headers) and data (sequences), bulk operations using standard text streaming tools (such as sed or awk) are impossible without including a parsing step, which may be error-prone and introduce friction in the development process. RESULTS: Here, we present FUSTA (FUse for faSTA), a software utility which makes use of the FUSE technology to expose a multiFASTA file as a hierarchy of virtual files, letting users operate directly on the sequences as independent virtual files through classical file manipulation methods. AVAILABILITY AND IMPLEMENTATION: FUSTA is freely available under the CeCILL-C (LGPLv3-compatible) license at https://github.com/delehef/fusta. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.