LOCAS

LOCAS assembles eukaryotic genomes from low-coverage short-read NGS data to detect sequence variation, including novel insertions and highly diverged regions.

Key Features:

• Mismatch-sensitive Overlap-Layout-Consensus: LOCAS employs an overlap-layout-consensus assembly strategy that is sensitive to mismatches to handle low-coverage short-read data.
• Homology-guided assembly: Performs homology-guided assembly of homologous regions by leveraging existing sequence similarity.
• De novo assembly of novel variations: Conducts de novo assembly after an initial alignment-consensus phase to reconstruct insertions and highly polymorphic regions.
• Performance on benchmark datasets: In evaluations on Arabidopsis 1001 Genomes Project data, LOCAS produced larger contigs, lower error rates, and faster runtimes than compared NGS assemblers and successfully assembled long insertions.

Scientific Applications:

• Population-scale low-coverage re-sequencing: Applicable to large re-sequencing projects such as the Human 1000 Genomes Project to detect genetic variation from many low-coverage samples.
• Discovery of novel insertions and highly diverged sequences: Enables detection and assembly of insertions and highly polymorphic or diverged regions in eukaryotic genomes from short-read data.

Methodology:

LOCAS applies a mismatch-sensitive overlap-layout-consensus approach with a two-phase workflow: a homology-guided assembly following an initial alignment-consensus step (phase 1) and a de novo assembly targeting insertions and highly polymorphic regions (phase 2).