Shasta

Shasta assembles de novo genomes from Oxford Nanopore technologies long-read sequencing data to enable rapid, high-contiguity assembly of human genomes.

Key Features:

• Rapid Assembly Process: Assembles a complete haploid human genome in under six hours on a single commercial compute node compared with previous approaches requiring ~150,000 CPU hours and several weeks of wall-clock time.
• High Contiguity and Coverage: Using PromethION nanopore sequencing, achieves approximately 63× coverage with read N50 around 42 kilobases and ~6.5× coverage for reads >100 kb with three flow cells per sample.
• Polishing Algorithms: Includes MarginPolish and HELEN to improve consensus accuracy to >99.9% identity (QV30) using only nanopore reads.
• Proximity-Ligation Sequencing Integration: Integrates proximity-ligation sequencing data to produce near chromosome-level scaffolds.

Scientific Applications:

• Human Genomic Studies: De novo assembly of human genomes for high-contiguity, high-accuracy reference generation.
• Comparative Genomics: Production of near chromosome-level scaffolds to support comparative analyses across samples or species.
• Clinical and Personalized Medicine: Rapid assembly to accelerate identification of genetic variants relevant to disease diagnosis and personalized treatment strategies.

Methodology:

Efficiently processes long reads from Oxford Nanopore sequencers.
Utilizes advanced algorithms for rapid assembly and polishing (including MarginPolish and HELEN).
Integrates additional sequencing data such as proximity-ligation reads to enhance scaffold resolution.