BreakAlign: a Perl program to align chimaeric (split) genomic NGS reads and allow visual confirmation of novel retroviral integrations.
BreakAlign: a Perl program to align chimaeric (split) genomic NGS reads and allow visual confirmation of novel retroviral integrations.
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DOI：
10.1186/s12859-022-04621-1
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发表时间：
2022-04-15
影响因子：
3
通讯作者：
Belshaw, Robert
中科院分区：
文献类型：
--
作者：
Marchi, Emanuele;Jones, Mathew;Klenerman, Paul;Frater, John;Magiorkinis, Gkikas;Belshaw, Robert
逆转录病毒通过将DNA拷贝整合到宿主染色体中进行复制。从基因组NGS数据中检测新的逆转录病毒整合物（不在宿主参考基因组序列中的逆转录病毒整合物）在生物信息学上具有挑战性，并且经常产生许多假阳性。一种常见的确认方法是目视检查跨越假定的新型逆转录病毒整合位点的嵌合（分裂）reads的排列。我们认为需要一个程序，通过产生包含病毒和宿主区域的多重排列来促进这一点。BreakAlign是一个Perl程序，它使用blastn生成这种多重对齐。除了NGS数据集和参考病毒序列外，该程序还需要(a)跨越假定整合的~ 500nt宿主基因组序列，或(b)在已安装的参考人类基因组副本中该假定整合的坐标（可自动处理多个整合）。BreakAlign可以从https://github.com/marchiem/breakalign免费获得，并附带了允许测试运行的示例文件。BreakAlign将确认并促进(a)内源性逆转录病毒的种系整合和(b)外源性逆转录病毒（如HIV和HTLV）的体细胞整合的特征。虽然开发用于基因组短读NGS（第二代）数据和逆转录病毒，但它也可用于长读（第三代）数据和任何具有至少一个保守侧翼区域的移动元件。在线版本包含补充材料，可在10.1186/s12859-022-04621-1获得。
Retroviruses replicate by integrating a DNA copy into a host chromosome. Detecting novel retroviral integrations (ones not in the reference genome sequence of the host) from genomic NGS data is bioinformatically challenging and frequently produces many false positives. One common method of confirmation is visual inspection of an alignment of the chimaeric (split) reads that span a putative novel retroviral integration site. We perceived the need for a program that would facilitate this by producing a multiple alignment containing both the viral and host regions that flank an integration. BreakAlign is a Perl program that uses blastn to produce such a multiple alignment. In addition to the NGS dataset and a reference viral sequence, the program requires either (a) the ~ 500nt host genome sequence that spans the putative integration or (b) coordinates of this putative integration in an installed copy of the reference human genome (multiple integrations can be processed automatically). BreakAlign is freely available from https://github.com/marchiem/breakalign and is accompanied by example files allowing a test run. BreakAlign will confirm and facilitate characterisation of both (a) germline integrations of endogenous retroviruses and (b) somatic integrations of exogenous retroviruses such as HIV and HTLV. Although developed for use with genomic short-read NGS (second generation) data and retroviruses, it should also be useful for long-read (third generation) data and any mobile element with at least one conserved flanking region. The online version contains supplementary material available at 10.1186/s12859-022-04621-1.
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DOI：
10.1126/science.1254194
发表时间：
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期刊：
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DOI：
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发表时间：
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影响因子：
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