CABOG

CABOG assembles whole-genome shotgun sequencing reads from mixed Sanger (ABI 3730) and 454 FLX pyrosequencing datasets into contigs and scaffolds for genome assembly.

Key Features:

• Hybrid Data Compatibility: Accommodates differences between ABI 3730 (Sanger) and 454 FLX (pyrosequencing) read types, including accuracy, coverage, read length, and paired-end protocols.
• Robustness: Handles homopolymer run length uncertainty, high read coverage, and heterogeneous read lengths typical of hybrid sequencing datasets.
• Contig Assembly Efficiency: Produces some of the longest contigs among tested assemblers and leverages mate constraints from paired-end reads to construct larger contigs and scaffolds.
• Validation and Accuracy: Validates assembled contigs and scaffolds against finished reference sequences and exhibits a low rate of contig mis-assembly that is mitigated by sufficient mate pair data.

Scientific Applications:

• Hybrid whole-genome assembly: Integrating Sanger (ABI 3730) and 454 FLX pyrosequencing data for de novo genome assembly in genomic research projects.

Methodology:

Implements modifications to the Celera Assembler to manage mixed Sanger and 454 FLX data, exploits mate constraints from paired-end reads to improve contig and scaffold construction, and validates assemblies against finished reference sequences.