IMSA: integrated metagenomic sequence analysis for identification of exogenous reads in a host genomic background.
IMSA: integrated metagenomic sequence analysis for identification of exogenous reads in a host genomic background.
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DOI：
10.1371/journal.pone.0064546
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Arron ST
中科院分区：
文献类型：
--
作者：
Dimon MT;Wood HM;Rabbitts PH;Arron ST
宏基因组学是研究不同环境中微生物基因组的一个快速发展的领域。宿主生物体内微生物序列的鉴定使得能够研究人类肠道、呼吸道和皮肤微生物群，并且已经允许鉴定疾病如默克尔细胞癌中的新型病毒。很少有公开可用的工具用于宏基因组高通量序列分析。我们提出了集成宏基因组序列分析（IMSA），一个灵活，快速，强大的计算分析管道，可供公众使用。IMSA从高通量数据集中获取输入序列，并使用用户定义的宿主数据库来筛选出宿主序列。然后，IMSA将过滤的读数与用户定义的通用数据库进行比对，以表征宿主背景中的外源读数。IMSA根据读取频率为分类的每个节点分配一个分数，并可以将其输出为适合聚类分析的分类报告或分类图（TaxMap）。IMSA还输出分配给感兴趣的分类单元的特定序列读数用于下游分析。我们证明了使用IMSA检测病原体和正常植物群内的序列数据从原发性人宫颈癌携带HPV 16，原发性人皮肤鳞状细胞癌携带HPV 16，CaSki细胞系携带HPV 16，和HeLa细胞系携带HPV 18。
Metagenomics, the study of microbial genomes within diverse environments, is a rapidly developing field. The identification of microbial sequences within a host organism enables the study of human intestinal, respiratory, and skin microbiota, and has allowed the identification of novel viruses in diseases such as Merkel cell carcinoma. There are few publicly available tools for metagenomic high throughput sequence analysis. We present Integrated Metagenomic Sequence Analysis (IMSA), a flexible, fast, and robust computational analysis pipeline that is available for public use. IMSA takes input sequence from high throughput datasets and uses a user-defined host database to filter out host sequence. IMSA then aligns the filtered reads to a user-defined universal database to characterize exogenous reads within the host background. IMSA assigns a score to each node of the taxonomy based on read frequency, and can output this as a taxonomy report suitable for cluster analysis or as a taxonomy map (TaxMap). IMSA also outputs the specific sequence reads assigned to a taxon of interest for downstream analysis. We demonstrate the use of IMSA to detect pathogens and normal flora within sequence data from a primary human cervical cancer carrying HPV16, a primary human cutaneous squamous cell carcinoma carrying HPV 16, the CaSki cell line carrying HPV16, and the HeLa cell line carrying HPV18.
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影响因子：
5.7
作者：
Lagier JC;Million M;Hugon P;Armougom F;Raoult D
通讯作者：
Raoult D
影响因子：
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Eloit, Marc
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Flemington, Erik K.
影响因子：
9.4
作者：
Yang, Jian;Yang, Fan;Jin, Qi
通讯作者：
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