Kijak Gustavo H, Pham Phuc, Sanders-Buell Eric, Harbolick Elizabeth A, Eller Leigh Anne, Robb Merlin L, Michael Nelson L, Kim Jerome H, Tovanabutra Sodsai
1 U.S. Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine , Bethesda, Maryland.
AIDS Res Hum Retroviruses. 2013 Oct;29(10):1361-4. doi: 10.1089/AID.2013.0175. Epub 2013 Aug 2.
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 .
新一代测序技术的出现为HIV-1的多样性和进化提供了新的见解，这就需要能够应用于病毒准种特征分析的生物信息学工具。在此，我们介绍Nautilus，这是一个用于分析HIV-1靶向深度测序数据的生物信息学软件包。DeepHaplo模块可确定每个位置的核苷酸碱基频率和读取深度，并根据同一下一代序列读取中多态性之间的连锁关系计算单倍型频率。Motifs模块在序列上下文和映射方向的背景下计算变异频率，当怀疑存在链偏倚时，这有助于验证多态性和单倍型。这两个模块均可通过一个用户友好的图形用户界面访问，该界面运行于Mac OS X（版本10.7.4或更高版本），并基于Python、JAVA和R脚本。可从www.hivresearch.org/research.php?ServiceID=5&SubServiceID=6获取Nautilus。
