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Nautilus: A bioinformatics package for the analysis of HIV type 1 targeted deep sequencing data

机译：Nautilus：用于分析HIV 1型靶向深度测序数据的生物信息学软件包

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摘要

The advent of next generation sequencing technologies is providing new insight into HIV-1 diversity and evolution, which has created the need for bioinformatics tools that could be applied to the characterization of viral quasispecies. Here we present Nautilus, a bioinformatics package for the analysis of HIV-1 targeted deep sequencing data. The DeepHaplo module determines the nucleotide base frequency and read depth at each position and computes the haplotype frequencies based on the linkage among polymorphisms in the same next generation sequence read. The Motifs module computes the frequency of the variants in the setting of their sequence context and mapping orientation, which allows for the validation of polymorphisms and haplotypes when strand bias is suspected. Both modules are accessed through a user-friendly GUI, which runs on Mac OS X (version 10.7.4 or later), and are based on Python, JAVA, and R scripts. Nautilus is available from www.hivresearch.org/research.php?ServiceID= 5&SubServiceID=6.
机译：下一代测序技术的出现为人们提供了对HIV-1多样性和进化的新见解，从而产生了对可用于表征病毒准种的生物信息学工具的需求。在这里，我们介绍Nautilus，这是一种用于分析HIV-1靶向深度测序数据的生物信息学软件包。 DeepHaplo模块确定每个位置的核苷酸碱基频率和读取深度，并基于同一下一代读取序列中多态性之间的联系计算单倍型频率。 Motifs模块在设置变体的序列上下文和定位方向时计算变体的频率，从而在怀疑有链偏向时允许验证多态性和单倍型。这两个模块都是通过用户友好的GUI访问的，该GUI运行在Mac OS X（版本10.7.4或更高版本）上，并且基于Python，JAVA和R脚本。 Nautilus可从www.hivresearch.org/research.php?ServiceID=5&SubServiceID=6获得。

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