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FASTAFS: file system virtualisation of random access compressed FASTA files.

Youri Hoogstrate1,2,3, Guido W Jenster4, Harmen J G van de Werken4,5,6

  • 1Department of Neurology, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands. yhoogstrate@erasmusmc.nl.

BMC Bioinformatics
|November 2, 2021
PubMed
Summary

FASTAFS virtualizes FASTA archives into the filesystem, enabling direct access to compressed sequence data and metadata. This user-friendly toolkit ensures backward compatibility and simplifies bioinformatics workflows.

Keywords:
FASTAFASTAFSFUSEIntegrityMetadataRandom accessVirtualisationZstd

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • The FASTA file format is a long-standing bioinformatics standard for polymeric sequence data.
  • Large FASTA files necessitate supplementary files for sequence identification and random access.
  • Existing compression tools for FASTA files lack direct content access and metadata synchronization, hindering software integration.

Purpose of the Study:

  • To develop a novel toolkit for efficient storage and access of compressed FASTA files.
  • To address limitations in random access and metadata management for archived sequence data.
  • To enhance software integration and usability in bioinformatics workflows.

Main Methods:

  • Implementation of a Linux-based toolkit (FASTAFS) utilizing Filesystem in Userspace (FUSE).
  • Virtualization of FASTA archive content, including DNA, RNA, and protein sequences, into the filesystem.
  • Integration of bit encodings and Zstandard (zstd) for fast random-access decompression.

Main Results:

  • FASTAFS provides synchronized virtualized metadata files and enables rapid random access to compressed FASTA data.
  • The toolkit offers system-wide instance tracking, file integrity verification, and instant scriptable access.
  • Compression ratios achieved by FASTAFS are comparable to state-of-the-art archival tools, with enhanced random access capabilities.

Conclusions:

  • FASTAFS presents a user-friendly, backward-compatible solution for accessing compressed FASTA files through filesystem virtualization.
  • The toolkit simplifies data access and format conversion without requiring code modifications across different programming languages.
  • Virtual filesystems offer a versatile layer for managing and accessing bioinformatics data formats efficiently.