GAM-NGS

GAM-NGS merges two or more genomic assemblies to improve contiguity and correctness of de novo assemblies by identifying corresponding loci via read alignments and resolving conflicts with a weighted graph.

Key Features:

• Assembly merging: Merges two or more genomic assemblies to produce a consolidated set of sequences.
• Block identification via read alignments: Identifies regions representing the same genomic locus (blocks) through alignments of reads.
• Weighted graph resolution: Organizes identified blocks into a weighted graph to optimally resolve local problematic areas during merging.
• No global contig alignment: Avoids reliance on global alignment between contigs when reconciling assemblies.
• Illumina multi-library support: Applicable to multi-library Illumina-based projects integrating diverse datasets.
• Contiguity and correctness improvement: Aims to enhance both contiguity and correctness of resulting assemblies.
• Empirical evaluation: Tested across six distinct datasets and compared with other assembly reconciliation tools, producing improved sequences when references were available.
• Computational efficiency: Requires substantially fewer computational resources than comparable tools according to reported tests.

Scientific Applications:

• Assembly reconciliation: Combine outputs from different assemblers to produce a more accurate consensus assembly.
• De novo genome assembly improvement: Improve contiguity and correctness of de novo assemblies from NGS data.
• Multi-library Illumina projects: Integrate and reconcile assemblies derived from multiple Illumina libraries.
• Reference-based validation: Produce improved and reliable sequence sets when reference sequences are available for evaluation.

Methodology:

Align reads to assemblies to identify blocks representing the same locus, organize blocks into a weighted graph, and use the graph to resolve local conflicts and merge assemblies without performing global contig alignment.