Chromonomer

Chromonomer integrates genome assemblies with genetic maps and optional conserved synteny to detect and correct assembly defects (for example from repetitive sequences or sequencing artifacts) and produce improved chromosome models (chromonomes).

Key Features:

• Map–assembly integration: Reconciles scaffold and local assembly order with genetic marker maps to identify discrepancies.
• Conserved synteny support: Optionally incorporates conserved synteny from related taxa to inform scaffold ordering and orientation.
• Marker discordance detection: Detects genetic markers that are out of sequence in the genetic map relative to their positions in the assembly.
• Scaffold correction: Identifies incorrectly assembled scaffolds and splits them as necessary to correct assembly errors indicated by the genetic map.
• Change tracking: Records and tracks changes made to both the assembly and the genetic map.
• Input flexibility: Accepts user-defined reference genomes and maps of genetic markers as inputs.
• Error targeting: Specifically addresses defects arising from repetitive sequences and sequencing or molecular artifacts that produce fragmented or chimeric assemblies.
• Chromonome construction: Produces improved chromosome models ("chromonomes") by integrating map and assembly data.

Scientific Applications:

• Assembly refinement: Correcting assembly errors in fragmented or chimeric genome assemblies.
• Chromosome-level assembly: Generating chromosome models (chromonomes) for downstream genomic analyses.
• Map–assembly reconciliation: Resolving conflicts between physical assemblies and genetic linkage maps to improve interpretation of genome structure.
• Comparative genomics: Using conserved synteny from related taxa to improve ordering and comparative analyses.
• Broad applicability: Applicable to genome assemblies and genetic maps with varying characteristics and quality levels.

Methodology:

Integrates genome assemblies with genetic maps and optional conserved synteny, detects markers discordant between map order and assembly positions, identifies and splits incorrectly assembled scaffolds, records changes to the assembly and map, and uses user-provided reference genomes and genetic marker maps as inputs.