GeneASIC NGSAAP is an ultra-fast NGS data analysis solution that excels not only in speed but also in accuracy. While GATK has been the gold standard for genomic analysis and has become even more powerful with the latest DRAGEN mapper integration, we aim to go beyond best practices. Our goal lies in continually developing and refining our algorithms to ensure accuracy evolves with each iteration. This ongoing improvement helps us stay ahead of emerging challenges in genomic research.
Here, we present our latest advancements in genomic secondary analysis algorithms.We improve F1 score very ilteration version last year as shown in Fig 1.
Figure 1: F1 score of GATK , GATK-DRAGEN and every version of GeneASIC NGSAAP
F1 score provides a balance between precision and recall,
The key improvement is in indel detection, a known challenge in alignment. By refining our algorithm to better handle homopolymers and tandem repeats, we’ve significantly improved accuracy in detecting insertions and deletions in Fig2.
The improvement in overall F1 score follows the same trend as the indel detection .
Figure 2: A bar chart comparing the INDEL F1 score of GATK, GATK-DRAGEN, and multiple versions of GeneASIC NGSAAP. The X-axis represents the tool or version, while the Y-axis represents the INDEL F1 score.
NGSAAP variant detection ability is accurate in other benchmark sample.
Our improvements are applicable to all benchmark samples. We have reanalyzed every benchmark sample and demonstrated superior performance. Fig3 shows lastest GeneASIC NGSAAP has best performance on each Novaseq 30X WGS. Average F1 score is 99.47%
Figure 3: A bar chart comparing the overall F1 score of NGSAAP, GATK, and GATK-DRAGEN across three different samples (HG002, HG003, HG004) using Illumina NovaSeq 30x WGS data. The X-axis represents the sample, while the Y-axis represents the F1 score.
NGSAAP variant detection performance on leading sequencing technologies.
NGSAAP, optimized for compatibility with Illumina, MGI, and Element sequencing technologies, consistently outperforms GATK-DRAGEN across various datasets. As demonstrated in Figure 4, NGSAAP’s superior performance is evident when using the HG002 sample and three distinct datasets: Illumina NovaSeq 30x WGS, MGIseq-2000 30x WGS, and Element AVITI 35x
Figure 4: Bar chart comparing the overall F1 score of NGSAAP and GATK-DRAGEN across three different sequencing technologies: Illumina NovaSeq, MGIseq-2000, and Element AVITI. The X-axis represents the sequencing technology, while the Y-axis represents the F1 score.
Conclusion
In summary, GeneASIC NGSAAP represents a significant advancement in NGS data analysis. Its speed（<30 min 30XWhole Genome Sequencing）, accuracy, and versatility make it a valuable tool for researchers seeking to accelerate their genomic research.
