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Mass Analyzers: Overview01:13

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Related Experiment Video

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Hybrid µCT-FMT imaging and image analysis
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MAFCO: a compression tool for MAF files.

Luís M O Matos1, António J R Neves1, Diogo Pratas1

  • 1Signal Processing Lab, IEETA/DETI, University of Aveiro, 3810-193 Aveiro, Portugal.

Plos One
|March 28, 2015
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Summary

Storing large genomic datasets is challenging. MAFCO is a new lossless compression tool specifically designed for Multiple Alignment Format (MAF) files, offering significant data size reduction compared to general-purpose tools like gzip.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Genomic sequencing costs are rapidly decreasing, leading to massive data generation.
  • Efficient storage solutions are crucial as storage costs do not decrease as rapidly as sequencing costs.
  • General-purpose compression tools like gzip are commonly used but suboptimal for genomic data.

Purpose of the Study:

  • To introduce MAFCO, a novel lossless compression tool.
  • To specifically address the compression of Whole Genome Alignments in MAF format.
  • To improve data compression efficiency for large-scale genomic datasets.

Main Methods:

  • Development of a specialized lossless compression algorithm.
  • Implementation of MAFCO tailored for Multiple Alignment Format (MAF) files.
  • Evaluation of MAFCO's compression performance against existing methods.

Main Results:

  • MAFCO achieves a compression gain of 34% to 57% over gzip.
  • MAFCO provides approximately 9% better compression than a recent dedicated method.
  • MAFCO demonstrates effectiveness on Whole Genome Alignments.

Conclusions:

  • MAFCO offers a significant improvement in compressing MAF files.
  • The tool provides a valuable solution for managing large genomic data storage.
  • MAFCO is freely available for non-commercial use, promoting wider adoption in research.