GPM

GPM integrates physical, optical, and genetic maps with next-generation sequencing assemblies to connect, edit, order, orient, and merge sequences into annotation-ready pseudomolecules that improve genome assembly quality.

Key Features:

• Integration of genomic signposts: Incorporates physical maps, optical maps, and genetic maps into draft assemblies to provide additional spatial and relational information for contigs and scaffolds.
• Semi-automated assembly editing: Connects loaded datasets through logical relationships to group, merge, order, and orient sequences within draft assemblies.
• Dataset linkage via logical relationships: Establishes explicit logical connections among sequence data and external mapping datasets to guide assembly refinement.
• Manual curation support: Enables manual intervention and curation of assembly components to resolve conflicts and refine structure.
• Production of annotation-ready pseudomolecules: Produces high-quality pseudomolecules suitable for downstream annotation and analysis.
• Addressing NGS fragmentation: Mitigates fragmented and inaccurate assemblies produced by next-generation sequencing by integrating complementary mapping datasets.

Scientific Applications:

• Gene annotation: Provides refined, contiguous assemblies that facilitate accurate structural and functional gene annotation.
• Comparative genomics: Generates improved assemblies for reliable genome-to-genome comparisons and synteny analyses.
• Evolutionary studies: Produces contiguous pseudomolecules that support analyses of genome evolution, structural variation, and phylogenomics.
• Downstream assembly analyses: Supplies annotation-ready assemblies for downstream analyses such as variant calling, functional genomics, and repeat characterization.

Methodology:

Logical connection of datasets via inherent relationships combined with automated algorithms and manual interventions to group, merge, order, and orient sequences, producing refined pseudomolecules.