FPSAC

FPSAC performs phylogenetic scaffolding of ancient bacterial contigs to reconstruct ancestral genome organization and correct ordering and orientation in ancient DNA assemblies.

Key Features:

• Adaptation for Ancient Genomes: Tailored to handle ancient DNA decay and fragmentation, enabling scaffolding of fragmented ancient bacterial contigs.
• Phylogenetic Approach: Uses phylogenetic information from extant genomes to infer ancestral genome organization for scaffolding.
• Efficiency and Speed: Performs rapid phylogenetic scaffolding suitable for large paleogenomic datasets.

Scientific Applications:

• Yersinia pestis Black Death assembly: Applied to assemble 2134 ancient contigs from the Yersinia pestis strain of the Black Death, producing a scaffold for the entire chromosome.
• Historical genomics and evolutionary biology: Enables analyses of structural evolution within bacterial clades and investigation of genomic changes over time.

Methodology:

Adapts existing computational paleogenomics techniques by comparing extant genomes to reconstruct ancestral genome organization and uses that reconstruction to scaffold ancient contigs, correcting ordering and orientation.