Sentieon致力于解决生物信息数据分析中的速度与准确度瓶颈，通过算法的深度优化和企业级的软件工程，大幅度提升NGS数据处理的效率、准确度和可靠性。自2015年的初始版本开始，Sentieon推出了包括比对到变异检测在内的完整二次分析的解决方案，可用于胚系突变检测和体细胞突变检测。
多年来，Sentieon软件被业内的制药企业、科研院所、临床医学、农业基因组等领域的用户广泛采用。为了让更多用户了解Sentieon在自己工作的领域的应用案例，INSVAST从已发表的项目中精选一些有代表性文章作为案例分享给大家。
本文通过分享4篇已发表文章来介绍Sentieon在农业基因组科研项目中的应用。
Cornell University
利用NGS测序生成新的葡萄基因组育种标记物
标题：Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus
发表期刊：Nature Communications
发表日期：2020年1月21日
主要作者单位：Cornell University
使用Sentieon模块：Sentieon BWA, DNAseq
Transferable DNA markers are essential for breeding and genetics. Here, we apply a marker strategy targeting the inferred Vitis core genome. Incorporating seven linked read de novo assemblies and three existing assemblies, adding shotgun genome sequences from 40 accessions enables identification of conserved core PCR primer binding sites flankingpoly-morphic haplotypes with high information content. From these target regions, we develop 2,000 rhAmpSeq markers as a PCR multiplex and validate the panel in four biparental populations spanning the diversity of the Vitis genus, showing transferability increases to 91.9%.
高粱单倍型数据库开启低深度全基因组测序应用，降低测序成本
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标题：A sorghum practical haplotype graph facilitates genome-wide imputation and cost-effective genomic prediction
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发表期刊：The Plant Genome
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发表日期：2020年1月4日
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主要作者单位：Cornell University
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使用Sentieon模块：Sentieon DNAseq
We developed a Sorghum bicolor Practical Haplotype Graph (PHG) pangenome database that stores haplotypes and variant information. The PHG called single nucleotide polymorphisms (SNPs) with 5.9% error at 0.01x coverage—only 3% higher than PHG error when calling SNPs from 8x coverage sequence. Mean prediction accuracies with PHG SNP calls range from .57–.73 and are similar to prediction accuracies obtained with genotyping-by-sequencing or targeted amplicon sequencing (rhAmpSeq) markers. This study demonstrates the use of a sorghum PHG to impute SNPs from low-coverage sequence data and shows that the PHG can unify genotype calls across multiple sequencing platforms.
全基因组测序揭示波斯核桃木的起源
标题：Phylogenomics Reveals an Ancient Hybrid Origin of the Persian Walnut
发表期刊：Molecular Biology and Evolution
发表日期：2019年6月4日
主要作者单位：北京师范大学
使用Sentieon模块：Sentieon DNAseq, GVCFTyper
The origin of Persian walnut (Juglans regia) has remained mysterious because in phylogenies it occupies an unresolved position between American black walnuts and Asian butternuts. We resequenced the whole genome of 80 individuals from 19 of the 22 species of Juglans and assembled the genome of its relatives Pterocarya stenoptera and Platycarya strobilacea. Using phylogenetic-network analysis of single-copy nuclear genes, genome-wide site pattern probabilities, and Approximate Bayesian Computation, we discovered that J. regia arose as a hybrid between the American and the Asian lineages.
玉米的性别特异性染色体重组特征探究
标题：High-resolution crossover mapping reveals similarities anddifferences of male and female recombination in maize
发表期刊：Nature Communications
发表日期：2018年6月18日
主要作者单位：University of Minnesota
使用Sentieon模块：DNAseq
Although many species exhibit large differences in CO numbers between sexes, sex-specific aspects of CO landscape are particularly poorly elucidated. Here, we conduct high-resolution CO mapping in maize. Our results show that CO numbers as well as their overall distribution are similar in male and female meioses. There are, nevertheless, dissimilarities at local scale. Our data suggest that sex-specific factors not only affect male–female CO number disparities but also cause fine differences in CO positions.
除了本文中精选的四篇发表文献之外，Sentieon在全球上百家科研机构以及农业育种公司中被广泛应用，从我们和用户的沟通中了解到，动植物的基因组往往在体积和复杂度方面远大于人类基因组，造成的二级分析时候计算通量的短缺。换用Sentieon软件之后，不但缓解了计算时间的瓶颈，由于Sentieon超越开源软件的稳定性和内存利用效率，在处理多倍型等大型基因组时还可以有效避免流程崩溃等问题。
