AlignGraph

AlignGraph improves de novo genome assemblies by using paired-end (PE) reads, preassembled contigs or scaffolds and alignments to closely related reference genomes to extend and join fragmented assemblies.

Key Features:

• Guided Assembly Enhancement: AlignGraph aligns paired-end (PE) reads and preassembled contigs or scaffolds to closely related reference genomes to identify potential extensions and connections within assemblies.
• PE Multipositional de Bruijn Graph: It constructs a PE multipositional de Bruijn graph that integrates positional information from alignments and PE reads to guide accurate extension of assemblies and reduce incorrect extensions or premature terminations.
• Performance Metrics Improvement: In evaluations, AlignGraph extended 28.7-62.3% of contigs for Arabidopsis thaliana and human, increasing N50 by 89.9-94.5% for A. thaliana and 80.3-165.8% for human assemblies.
• Application to Published Genomes: It increased the N50 of extendable scaffolds by 86.6% for the Arabidopsis strain Landsberg.

Scientific Applications:

• Genome assembly refinement: Improves completeness and continuity of de novo genome assemblies across organisms such as Arabidopsis thaliana and human.
• Comparative genomics and evolutionary analysis: Uses related reference genomes to enable more accurate reconstruction of genomic sequences for studying genetic variation and evolutionary relationships among species.

Methodology:

AlignGraph aligns paired-end reads and preassembled contigs or scaffolds to a reference genome and constructs a PE multipositional de Bruijn graph that incorporates positional information from alignments and PE reads to guide extension and joining of contigs or scaffolds.