Supernova

Supernova assembles diploid de novo genomes from 10x Genomics Chromium Linked-Reads to produce phased maternal and paternal chromosome sequences for accurate representation of diploid genomes.

Key Features:

• De novo diploid assembly: Separately assembles maternal and paternal chromosomes rather than producing a single collapsed consensus sequence.
• Chromium Linked-Reads support: Leverages 10x Genomics Chromium microfluidic partitioning of approximately 1 ng of high molecular weight DNA to generate linked-read libraries that retain long-range information and haplotype phase.
• Pushbutton algorithm: Implements a novel "pushbutton" algorithm for automated assembly processing.
• Contiguity and phasing metrics: Produces contigs exceeding 100 kb, phase blocks longer than 2.5 Mb, and scaffolds beyond 15 Mb.
• Novel sequence recovery: Assembles sequences that may be absent from reference genomes.
• Computational performance: Typical assembly completes in approximately two days on a single server.

Scientific Applications:

• Personalized medicine: Enables detection and representation of individual-specific variants and haplotypes for clinical genomics analyses.
• Population genetics: Facilitates haplotype-resolved comparative analyses across individuals and populations.
• Evolutionary studies: Supports investigation of structural variation and novel sequences relevant to evolutionary biology.
• Genetic variation discovery: Improves identification of phased variants and structural differences that are obscured by consensus assemblies.

Methodology:

Performs de novo assembly of linked-read data using a "pushbutton" algorithm to produce phased diploid assemblies by separately assembling maternal and paternal chromosomes into contigs, phase blocks, and scaffolds; typical runtime reported as ~2 days on a single server.