misSEQuel

misSEQuel identifies misassembly errors in draft genome assemblies by detecting extensively and locally misassembled contigs using paired-end sequence reads together with stimulated and real optical mapping data.

Key Features:

• Detection of extensively misassembled contigs: Detects extensively misassembled contigs within genome assemblies.
• Detection of locally misassembled contigs: Detects locally misassembled contigs within genome assemblies.
• Paired-end sequence read support: Utilizes paired-end sequence reads to support misassembly detection.
• Optical mapping integration: Integrates stimulated and real optical mapping data to identify breakpoints associated with assembly errors.
• Post-processing compatibility: Operates as a post-processing tool compatible with any genome assembler.

Scientific Applications:

• Francisella tularensis: Applied to F. tularensis assemblies, detecting over 54% of extensively misassembled contigs and more than 60% of locally misassembled contigs.
• Loblolly pine (Pinus taeda): Applied to loblolly pine assemblies, identifying between 31% to 100% of extensively misassembled contigs and 57% to 73% of locally misassembled contigs.
• Rice (Oryza sativa): Using real optical mapping data on O. sativa, detected 75% of extensively misassembled contigs and 100% of locally misassembled contigs.
• Budgerigar (Melopsittacus undulatus): Using real optical mapping data on M. undulatus, detected 77% of extensively misassembled contigs and 80% of locally misassembled contigs.

Methodology:

Leverages paired-end sequence reads together with stimulated and real optical mapping data to detect extensively and locally misassembled contigs and to identify breakpoints associated with assembly errors.