RACA

RACA assembles NGS-derived sequence scaffolds into ordered and oriented chromosome fragments using comparative genome information and paired-end reads to enable chromosome-scale reconstruction for studies of genome structure and evolution.

Key Features:

• Comparative genome guidance: RACA utilizes a reference assembly from a closely related species alongside outgroup genomes to guide scaffold ordering and orientation.
• Paired-end reads utilization: RACA incorporates paired-end reads to improve the reliability of scaffold arrangement and linkage evidence.
• Ordering and orientation: RACA orders and orients sequence scaffolds generated by NGS into longer chromosomal fragments.
• Compatibility with de novo assemblers: The algorithm is compatible with a wide variety of de novo assemblers and has been applied to SOAPdenovo scaffolds.
• Experimental validation: RACA's assembly predictions have been experimentally validated by PCR.

Scientific Applications:

• Chromosome reconstruction: RACA reconstructs chromosome fragments from complex genomes, exemplified by reconstruction of 60 fragments from 1,434 SOAPdenovo scaffolds in Tibetan antelope (Pantholops hodgsonii).
• Comparative genomics and chromosome evolution: RACA enables identification of homology between reconstructed fragments and complete chromosomes, such as 16 fragments homologous to complete cattle chromosomes, facilitating studies of genome rearrangements and evolution.

Methodology:

RACA uses a reference assembly from a closely related species and outgroup genomes, incorporates paired-end read information, and orders and orients NGS-derived scaffolds while remaining compatible with various de novo assemblers (e.g., SOAPdenovo).