TGNet

TGNet visualizes and assesses de novo genome assembly quality by summarizing alignments between genome scaffolds and independently derived transcriptome assemblies using Cytoscape.

Key Features:

• Visualization: Uses Cytoscape to visually summarize alignments between genome scaffolds and transcriptome sequences.
• Quality assessment: Detects discrepancies between genome scaffolds and independently derived transcriptome assemblies to evaluate scaffold integrity.
• Table generation from FASTA: Produces visualization-ready tables from FASTA sequence files and scaffolding information for downstream summarization.
• Support for complex assemblies: Targets de novo genome assemblies composed of many contigs and scaffolds for scaffold confirmation and improvement.

Scientific Applications:

• Identifying inconsistencies: Detects errors or misassemblies within genome scaffolds by comparison to transcriptome data.
• Confirming contig order: Verifies the arrangement of contigs within scaffolds using independent transcriptome alignments.
• Extending scaffolds: Supports extension and refinement of scaffolds where transcriptome evidence indicates contiguous sequence.
• Assembly validation in de novo projects: Applies transcriptome-to-genome comparisons to validate scaffold integrity in de novo genome sequencing projects.

Methodology:

Visualization-ready tables are generated from FASTA sequence files and scaffolding information; independently derived transcriptome sequences are aligned to the genome; alignments are visually summarized in Cytoscape to identify inconsistencies and confirm scaffold arrangements, with a demonstration on Solenopsis invicta reporting inconsistencies in 7% of scaffolds, confirmed contig order in 20%, and extended 16% of scaffolds.