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seq-seq-pan: building a computational pan-genome data structure on whole genome alignment.

Christine Jandrasits1, Piotr W Dabrowski1, Stephan Fuchs2

  • 1Robert Koch Institute, Nordufer 20, Berlin, 13353, Germany.

BMC Genomics
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Summary

The seq-seq-pan framework addresses limitations in representing genomic diversity by creating composite, linear whole genome alignments. This approach enhances pan-genomics and offers a fast alternative for aligning closely related genomes.

Keywords:
Data structurePan-genomeWhole genome alignment

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Next-generation sequencing generates vast genomic data, including multiple genomes per species, challenging traditional single-reference genome approaches.
  • Current methods using a single reference genome and variations fail to capture full species diversity and introduce bias.
  • A need exists for composite genome representations compatible with existing annotation and analysis tools, while remaining accessible and extendable.

Purpose of the Study:

  • To introduce seq-seq-pan, a novel framework for constructing and managing whole genome alignments.
  • To enable the representation of multiple genomes in a unified, linear format suitable for downstream analyses.
  • To facilitate the dynamic updating of genome sets and optimize alignment for pan-genomic applications.

Main Methods:

  • The seq-seq-pan framework employs a sequential workflow for adding/removing genomes and constructing whole genome alignments.
  • Alignment optimization focuses on generating a representative linear presentation of the aligned genome set.
  • The workflow is designed for compatibility with existing data sources and sequence analysis methods.

Main Results:

  • seq-seq-pan provides methods for dynamic updates to aligned genome sets.
  • The framework generates optimized, linear whole genome alignments suitable for annotation and downstream analysis.
  • The sequential workflow offers a fast alternative for aligning closely related genomes.

Conclusions:

  • seq-seq-pan enables the use of whole genome alignment in pan-genomics through dynamic updates and optimized processing.
  • The framework serves as a rapid alternative to existing whole genome aligners for closely related species.
  • seq-seq-pan is freely available, promoting broader adoption in genomic research.