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MUMmer4: A fast and versatile genome alignment system.

Guillaume Marçais1,2, Arthur L Delcher3, Adam M Phillippy4

  • 1Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America.

Plos Computational Biology
|January 27, 2018
PubMed
Summary
This summary is machine-generated.

MUMmer4, a new genome alignment tool, overcomes previous size limitations using a 48-bit suffix array and parallel processing. This enhanced system efficiently aligns large genomes, like human and chimpanzee, improving genomic analysis capabilities.

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • MUMmer (Multicopy Unique Molecular Marker) and its nucmer aligner are widely used in genomics.
  • MUMmer version 3 (released in 2004) has limitations for large genomes and datasets.
  • Previous versions struggled with the scale of modern genomic data.

Purpose of the Study:

  • Introduce MUMmer4, a significantly improved version of the MUMmer system.
  • Address limitations of MUMmer3 concerning genome size and processing speed.
  • Enhance capabilities for aligning large genomes and sequence datasets.

Main Methods:

  • Replaced the 32-bit suffix tree with a 48-bit suffix array to handle larger inputs.
  • Implemented parallel processing for input query sequences to increase speed.
  • Evaluated performance on large genome alignments, including human and chimpanzee genomes.

Main Results:

  • MUMmer4 supports input sizes up to 141 Terabase pairs (Tbp), accommodating biologically realistic sequence lengths.
  • The nucmer aligner in MUMmer4 efficiently aligns large genomes, demonstrating 98% identity between human and chimpanzee genomes across 96% of their length.
  • MUMmer4 can align reads to reference genomes, though with lower sensitivity than specialized tools.

Conclusions:

  • MUMmer4 overcomes the genome size constraints of previous versions through architectural and processing enhancements.
  • The new version offers significant improvements in speed and scalability for genome alignment tasks.
  • MUMmer4 provides a versatile and powerful tool for various genomic sequence alignment applications, including large-scale comparisons and read mapping.