PhrapUMD

PhrapUMD improves assembly quality of whole-genome shotgun (WGS) sequencing data by identifying repeat k-mer–based reliable overlaps and incorporating them into modified Phrap/Atlas assemblies to produce higher-quality draft genome assemblies.

Key Features:

• Reliable Overlaps Algorithm: Identifies "reliable" overlaps between sequencing reads by detecting repeat k-mers that confound assembly.
• 5-pass UMD Overlapper: Executes five passes to identify overlaps, correct base-caller errors, and perform additional trimming.
• Vector End Examination and Trimming: Detects and trims vector ends from sequencing reads to remove non-genomic sequence.
• Quality-Based Trimming: Trims reads based on quality scores to retain high-quality sequence for assembly.
• Integration with Phrap: Modifies the Phrap assembler to construct assemblies using only the identified reliable overlaps.
• Integration with Atlas Assembler: Interfaces with the Baylor College of Medicine Atlas assembler to further refine assemblies.

Scientific Applications:

• Draft genome assembly improvement: Enhances draft genome assemblies from WGS data by reducing assembly errors and improving coverage.
• BAC assembly for Rattus norvegicus: Applied with Atlas to Rattus norvegicus BACs, increasing finished-sequence coverage from 93.4% to 96.3% and reducing the base error rate from 4.5 to 1.1 errors per 10,000 bases.

Methodology:

Identify and trim vector ends, perform quality-based trimming, process reads through a 5-pass UMD Overlapper to find overlaps, correct base-caller errors and apply additional trimming, detect repeat k-mers to select reliable overlaps, modify Phrap to use only those overlaps, and integrate results with the Atlas assembler.