GEAN

GEAN performs genome annotation lift over using a weighted sequence alignment strategy to enable precise base-pair resolution alignment and variant calling across de novo assemblies, whole-genome resequencing, and RNA-seq data.

Key Features:

• Zebraic Striped Dynamic Programming Algorithm: Implements the Zebraic Striped Dynamic Programming algorithm that assigns different weights to genetic features to improve alignment accuracy.
• Weighted sequence alignment: Applies weighted sequence alignment to mitigate inconsistent alignments that can obscure functional impact predictions, particularly in plant species.
• Complement to standard approaches: Complements traditional sequence alignment methods to enhance accuracy when analyzing highly diverse individuals across plant and animal genomes.
• Lift over anchors for base-pair resolution: Uses lift over of genome annotations as anchors to perform base-pair resolution genome-wide sequence alignment and variant calling in de novo assembly contexts.
• Haplotype diversity comparison: Enables comparison of haplotype diversity across assemblies or individuals.
• Functional annotation refinement: Refines functional annotation of genetic variants to improve interpretation of variant effects.
• Annotation of de novo assemblies: Supports annotation transfer to de novo assembly genome sequences.
• Detection of homologous syntenic blocks: Identifies homologous syntenic blocks for comparative genomics analyses.
• Gene expression quantification improvement: Improves gene expression quantification using RNA-seq data by leveraging lifted annotations.
• Unification of genomic variants: Unifies genomic variants to facilitate population genetic analysis.

Scientific Applications:

• Population genetics: Enables unified variant sets and comparative analyses across individuals and populations using de novo assemblies and resequencing data.
• Comparative genomics: Supports detection of syntenic blocks and haplotype diversity comparisons across species or accessions.
• Functional genomics: Improves interpretation of variant functional impacts and refines gene models for downstream functional studies.
• Transcript quantification: Enhances RNA-seq–based gene expression quantification by providing lifted, assembly-specific annotations.
• Genome annotation transfer: Facilitates transferring annotations to de novo assembled genomes for downstream analyses.

Methodology:

Performs weighted sequence alignment using the Zebraic Striped Dynamic Programming algorithm that assigns different weights to genetic features and uses lifted genome annotations as anchors for base-pair resolution alignment and variant calling.