RePS

RePS performs whole-genome shotgun (WGS) assembly by identifying and removing exact 20-mer repeats prior to Phrap-based assembly with scaffolding to improve assemblies of repeat-rich genomes.

Key Features:

• Exact 20-mer repeat removal: Explicitly identifies and removes 20-mers that occur as exact repeats in shotgun sequencing data before assembly.
• Phrap integration: Conducts assembly using Phrap after repeat masking.
• Per-base error probabilities: Leverages established software to compute meaningful error probabilities for each base.
• Scaffolding with clone-end pairing: Integrates clone-end-pairing information to construct scaffolds that order and orient contigs.
• Low-coverage performance: Produces reasonable assemblies at 4x–6x coverage.
• High-repeat handling: Designed to handle genomes with high exact-repeat content, demonstrated up to 42.2% in human and rice datasets.

Scientific Applications:

• Whole-genome shotgun assembly: Assembly of WGS shotgun sequencing data, especially for repeat-rich genomes.
• Low-coverage assembly studies: Generation of assemblies from datasets with 4x–6x coverage.
• Complex genome analysis: Application to genomes with high fractions of exact repeats, as observed in human and rice.

Methodology:

Identify and remove exact 20-mer repeats prior to assembly; compute per-base error probabilities using established software; perform Phrap-based assembly on repeat-masked data; integrate clone-end-pairing to build scaffolds that order and orient contigs.