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FUSTA: leveraging FUSE for manipulation of multiFASTA files at scale
Franklin Delehelle1, Hugues Roest Crollius1
1Département de biologie, Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Paris 75005, France.
Bioinformatics Advances
|January 30, 2023
Summary
Large biological sequence files (multiFASTA) are difficult to manage. FUSTA software presents a solution by exposing these files as virtual files for easier manipulation.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- FASTA files are standard for biological sequences.
- MultiFASTA files present challenges in size and data manipulation.
- Current tools struggle with large, concatenated sequence data.
Purpose of the Study:
- To address the limitations of handling large multiFASTA files.
- To provide a more efficient method for biological sequence data management.
- To simplify bulk operations on biological sequences.
Main Methods:
- Developed FUSTA (FUse for faSTA) software.
- Utilized FUSE (Filesystem in Userspace) technology.
- Exposed multiFASTA files as a hierarchy of virtual files.
Main Results:
- FUSTA allows direct manipulation of sequences as independent virtual files.
- Overcomes limitations of standard text-editing and streaming tools.
- Enables classical file manipulation methods on sequence data.
Conclusions:
- FUSTA offers a practical solution for managing large multiFASTA datasets.
- Simplifies bioinformatics workflows by improving data accessibility.
- Enhances the efficiency of biological sequence analysis.
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