Scarpa

Scarpa scaffolds genome assemblies by ordering and orienting contigs to facilitate gap identification and finishing of draft assemblies.

Key Features:

• Algorithmic approach: Integrates fixed-parameter tractable algorithms and bounded algorithms with Linear Programming to generate near-optimal scaffolds.
• Contig ordering and orientation: Produces ordered and oriented scaffolds that are reported to be longer or of similar length while maintaining high accuracy compared to other scaffolders.
• Misassembly detection: Detects and reports misassembled contigs during the scaffolding process.
• Input compatibility: Accepts mappings from NGS read mappers in SAM format and is compatible with virtually any genome assembler.
• Multiple libraries support: Handles multiple sequencing libraries for scaffolding.
• Insert size estimation: Provides an option to estimate insert size distributions directly from data.
• Empirical evaluation: Performance validated on real datasets and on a simulated diploid genome.

Scientific Applications:

• Draft assembly finishing: Facilitates completion of draft genomes by ordering contigs and identifying gaps for subsequent closure.
• Assembly quality improvement: Improves assembly reliability by identifying misassembled contigs for correction.
• Evaluation of diploid assemblies: Applied to simulated diploid genome data to assess scaffolding performance in diploid contexts.

Methodology:

Integrates fixed-parameter tractable and bounded algorithms with Linear Programming, accepts SAM-format mappings from NGS read mappers, can estimate insert size distributions from data, and identifies misassembled contigs during scaffolding.