ASAP 2: a pipeline and web server to analyze marker gene amplicon sequencing data automatically and consistently.
ASAP 2: a pipeline and web server to analyze marker gene amplicon sequencing data automatically and consistently.
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DOI：
10.1186/s12859-021-04555-0
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发表时间：
2022-01-06
影响因子：
3
通讯作者：
Imanian B
中科院分区：
文献类型：
--
作者：
Tian R;Imanian B
16 S rDNA等标记基因的扩增子测序已被广泛应用于微生物群落的调查和表征。然而，复杂的数据分析需要许多干扰的手动步骤，往往导致结果不一致。在这里，我们开发了一个流水线，扩增子序列分析流水线2（ASAP 2），以自动化和滑动通过过程，而无需通常的手动检查和用户的干扰，例如，在检测条形码方向，选择高质量的读段区域，以及确定重新定位深度等等。该流水线集成了所有分析过程，例如导入数据、解复用、汇总读取概况、修整质量、去噪、去除嵌合序列和制作特征表等。管道接受多种文件格式作为输入，包括多路复用或解复用、双端或单端、内部或外部条形码以及原始或中间数据（例如，特征表）。产出包括分类学分类、α/β多样性、群落组成、排序分析和统计检验。ASAP 2支持合并多个测序运行，这有助于整合和比较来自不同来源（公共数据库和合作者）的数据。我们的流水线最大限度地减少了手动干扰，并自动一致地运行基于扩增子序列变体（ASV）的扩增子测序分析。我们的Web服务器可帮助无法访问高性能计算机（HPC）或生物信息学技能有限的研究人员。可以分别在https://github.com/tianrenmaogithub/asap2和https：//hts.iit.edu/asap2访问管道和网络服务器。在线版本包含补充材料，可通过10.1186/s12859-021-04555-0获得。
Amplicon sequencing of marker genes such as 16S rDNA have been widely used to survey and characterize microbial community. However, the complex data analyses have required many interfering manual steps often leading to inconsistencies in results. Here, we have developed a pipeline, amplicon sequence analysis pipeline 2 (ASAP 2), to automate and glide through the processes without the usual manual inspections and user’s interference, for instance, in the detection of barcode orientation, selection of high-quality region of reads, and determination of resampling depth and many more. The pipeline integrates all the analytical processes such as importing data, demultiplexing, summarizing read profiles, trimming quality, denoising, removing chimeric sequences and making the feature table among others. The pipeline accepts multiple file formats as input including multiplexed or demultiplexed, paired-end or single-end, barcode inside or outside and raw or intermediate data (e.g. feature table). The outputs include taxonomic classification, alpha/beta diversity, community composition, ordination analysis and statistical tests. ASAP 2 supports merging multiple sequencing runs which helps integrate and compare data from different sources (public databases and collaborators). Our pipeline minimizes hands-on interference and runs amplicon sequence variant (ASV)-based amplicon sequencing analysis automatically and consistently. Our web server assists researchers that have no access to high performance computer (HPC) or have limited bioinformatics skills. The pipeline and web server can be accessed at https://github.com/tianrenmaogithub/asap2 and https://hts.iit.edu/asap2, respectively. The online version contains supplementary material available at 10.1186/s12859-021-04555-0.
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影响因子：
48
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