Medical Research Council Centre for Medical Mycology at the University of Exeter, Exeter, UK.
BMC Bioinformatics. 2021 Nov 22;22(1):560. doi: 10.1186/s12859-021-04473-1.
Identifying haplotypes is central to sequence analysis in diploid or polyploid genomes. Despite this, there remains a lack of research and tools designed for physical phasing and its downstream analysis.
HaplotypeTools is a new toolset to phase variant sites using VCF and BAM files and to analyse phased VCFs. Phasing is achieved via the identification of reads overlapping ≥ 2 heterozygous positions and then extended by additional reads, a process that can be parallelized across a computer cluster. HaplotypeTools includes various utility scripts for downstream analysis including crossover detection and phylogenetic placement of haplotypes to other lineages or species. HaplotypeTools was assessed for accuracy against WhatsHap using simulated short and long reads, demonstrating higher accuracy, albeit with reduced haplotype length. HaplotypeTools was also tested on real Illumina data to determine the ancestry of hybrid fungal isolate Batrachochytrium dendrobatidis (Bd) SA-EC3, finding 80% of haplotypes across the genome phylogenetically cluster with parental lineages BdGPL (39%) and BdCAPE (41%), indicating those are the parental lineages. Finally, ~ 99% of phasing was conserved between overlapping phase groups between SA-EC3 and either parental lineage, indicating mitotic gene conversion/parasexuality as the mechanism of recombination for this hybrid isolate. HaplotypeTools is open source and freely available from https://github.com/rhysf/HaplotypeTools under the MIT License.
HaplotypeTools is a powerful resource for analyzing hybrid or recombinant diploid or polyploid genomes and identifying parental ancestry for sub-genomic regions.
在二倍体或多倍体基因组中，鉴定单倍型是序列分析的核心。尽管如此，仍然缺乏专门用于物理定相及其下游分析的研究和工具。
HaplotypeTools 是一个新的工具集，用于使用 VCF 和 BAM 文件对变体位点进行定相，并分析定相的 VCF。通过识别重叠≥2 个杂合位置的读取，并通过额外的读取进行扩展来实现定相，这个过程可以在计算机集群上进行并行化。HaplotypeTools 包括各种用于下游分析的实用脚本，包括交叉检测和将单倍型放置到其他谱系或物种的系统发育位置。HaplotypeTools 针对 WhatsHap 进行了准确性评估，使用模拟的短读和长读，证明了更高的准确性，尽管单倍型长度有所降低。HaplotypeTools 还在真实的 Illumina 数据上进行了测试，以确定杂交真菌分离物 Batrachochytrium dendrobatidis (Bd) SA-EC3 的祖先，发现基因组中 80%的单倍型与亲本谱系 BdGPL（39%）和 BdCAPE（41%）在系统发育上聚类，表明它们是亲本谱系。最后，在 SA-EC3 与任何一个亲本谱系之间的重叠相位组之间，约 99%的相位保持不变，表明有丝分裂基因转换/假两性生殖是该杂交分离物重组的机制。HaplotypeTools 是一个开源工具，可以从 https://github.com/rhysf/HaplotypeTools 免费获得，遵循麻省理工学院的许可协议。
HaplotypeTools 是分析杂种或重组二倍体或多倍体基因组以及识别亚基因组区域亲本祖先的强大资源。
