NGSEP

NGSEP performs genomic variant detection, genotyping, and downstream analysis from high-throughput sequencing data to support genetic-based diagnostics and genomic selection.

Key Features:

• Accurate Variant Calling: Identifies genomic variants across diverse species and sequencing protocols with high fidelity for medical diagnostics and agricultural applications.
• Efficient Realignment Algorithms: Implements advanced realignment and haplotype clustering algorithms for reads spanning indels and short tandem repeats (STRs) to reduce alignment-related inaccuracies.
• Benchmarked Performance: Benchmarking on real data from three sequencing protocols and four species with varying repetitive element distributions demonstrated improved accuracy and efficiency compared to existing software.

Scientific Applications:

• Medical Diagnostics: Precise variant calling enables identification of genetic disorders and predispositions.
• Agricultural Genomics: Reliable detection of beneficial variants supports genomic selection in plant and animal breeding for crop and livestock improvement.

Methodology:

Computational methods include read realignment and haplotype clustering to address sequencing errors and inaccuracies associated with repetitive elements such as STRs.