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哈比：一种用于处理单倍型标记连接读段数据的流程。

Harpy: a pipeline for processing haplotagging linked-read data.

作者信息

Dimens Pavel V, Franckowiak Ryan P, Iqbal Azwad, Grenier Jennifer K, Munn Paul R, Therkildsen Nina Overgaard

机构信息

Department of Natural Resources and the Environment, Cornell University, Ithaca, NY 14853, United States.

Genomics Innovation Hub, Biotechnology Resource Center, Cornell University, Ithaca, NY 14853, United States.

出版信息

Bioinform Adv. 2025 Jun 5;5(1):vbaf133. doi: 10.1093/bioadv/vbaf133. eCollection 2025.

DOI:10.1093/bioadv/vbaf133
PMID:40575478
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12198493/
Abstract

MOTIVATION

Haplotagging is a method for linked-read sequencing, which leverages the cost-effectiveness and throughput of short-read sequencing while retaining part of the long-range haplotype information captured by long-read sequencing. Despite its utility and advantages over similar methods, existing linked-read analytical pipelines are incompatible with haplotagging data.

RESULTS

We describe Harpy, a modular and user-friendly software pipeline for processing all stages of haplotagged linked-read data, from raw sequence data to phased genotypes and structural variant detection.

AVAILABILITY AND IMPLEMENTATION

https://github.com/pdimens/harpy.

摘要

动机

单倍型标记是一种用于连接读取测序的方法，它利用了短读长测序的成本效益和通量，同时保留了长读长测序所捕获的部分长程单倍型信息。尽管它具有实用性且优于类似方法，但现有的连接读取分析流程与单倍型标记数据不兼容。

结果

我们描述了Harpy，这是一个模块化且用户友好的软件流程，用于处理单倍型标记连接读取数据的各个阶段，从原始序列数据到定相基因型和结构变异检测。

可用性和实现方式

https://github.com/pdimens/harpy 。

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本文引用的文献

1
A survey of algorithms for the detection of genomic structural variants from long-read sequencing data.长读测序数据中基因组结构变异检测算法研究综述。
Nat Methods. 2023 Aug;20(8):1143-1158. doi: 10.1038/s41592-023-01932-w. Epub 2023 Jun 29.
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: fast and scalable deconvolution of linked-read sequencing data.：对连接读长测序数据进行快速且可扩展的反卷积分析
Bioinform Adv. 2022 Sep 26;2(1):vbac068. doi: 10.1093/bioadv/vbac068. eCollection 2022.
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Strobealign: flexible seed size enables ultra-fast and accurate read alignment.Strobealign：灵活的种子大小可实现超快速和准确的读取对齐。
Genome Biol. 2022 Dec 15;23(1):260. doi: 10.1186/s13059-022-02831-7.
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Read-Based Phasing and Analysis of Phased Variants with WhatsHap.基于读段的相位分析和 WhatsHap 分析相变异构体。
Methods Mol Biol. 2023;2590:127-138. doi: 10.1007/978-1-0716-2819-5_8.
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Haplotype tagging reveals parallel formation of hybrid races in two butterfly species.单体型标记揭示了两种蝴蝶物种中杂种种族的平行形成。
Proc Natl Acad Sci U S A. 2021 Jun 22;118(25). doi: 10.1073/pnas.2015005118.
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Twelve years of SAMtools and BCFtools.SAMtools 和 BCFtools 十二年。
Gigascience. 2021 Feb 16;10(2). doi: 10.1093/gigascience/giab008.
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Haplotype threading: accurate polyploid phasing from long reads.单体型连接：长读长准确进行多倍体相位分析。
Genome Biol. 2020 Sep 21;21(1):252. doi: 10.1186/s13059-020-02158-1.
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Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information.超微量单管连接读取文库方法使短读长第二代测序系统能够常规地生成高度准确和经济的长程测序信息。
Genome Res. 2020 Jun;30(6):898-909. doi: 10.1101/gr.260380.119. Epub 2020 Jun 15.
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Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly.高效且独特的第二代测序读长 DNA 分子 cobarcoding，实现经济高效、准确的测序、单倍型分析和从头组装。
Genome Res. 2019 May;29(5):798-808. doi: 10.1101/gr.245126.118. Epub 2019 Apr 2.
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fastp: an ultra-fast all-in-one FASTQ preprocessor.fastp：一个超快速的一体化 FASTQ 预处理程序。
Bioinformatics. 2018 Sep 1;34(17):i884-i890. doi: 10.1093/bioinformatics/bty560.