Decard: Cc11 Dataset

Data files for use with DECARD, as described in: Golob JL, Margolis E, Hoffman NG, Fredricks DN. <strong>Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities.</strong> BMC Bioinformatics. 2017 May 30;18(1):283. PMCID: PMC5450146 Contents:<br> - 16S_SSU.tar.bz2 Filtered full-length repository reads culled from NCBI 16S microbial bioproject and Silva. These are the templates to use when generating a community - CC11.tar.bz2 Reads for the CC11 family of 100 synthetic communities use for our BMC Bioinformatics publication.<br> 454 is for reads for simulated 454 pyrosequencing, amplified with the HMP 454 primers.<br> illumina is for miseq-like paired end reads, amplified with the EMP primers.<br> For each there are no error and reads with simulated error and a map file (specifying the community for each sequence ID<br> and the "true" source sequence for each read. - CC11_targets.csv<br> A target file, to be used with DECARD to recreate the CC11 communities, using the culled reads in 16S_SSU.tar.bz2 and primer sequences of your choosing. This can be used to test different primer sets.<br> <br> - CC11_targets.tre<br> The "true" phylogenetic tree for the full-length 16S sequences used in all of the CC11 communities, in Newick format and suitable for packages like Phyloseq to calculate "true" DPCoA or (weighted) UniFrac pairwise distances between the communities本数据集为适配DECARD工具的数据文件，相关研究详见以下文献： Golob JL, Margolis E, Hoffman NG, Fredricks DN. 《评估基于扩增子的微生物组计算流程对模拟人体肠道微生物群落的准确性》(Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities). BMC Bioinformatics. 2017年5月30日;18(1):283. PMCID: PMC5450146 数据集内容如下： - 16S_SSU.tar.bz2：从美国国家生物技术信息中心（National Center for Biotechnology Information, NCBI）16S微生物生物项目与Silva数据库中筛选得到的全长测序读段，可作为生成模拟微生物群落的参考模板。 - CC11.tar.bz2：包含本BMC Bioinformatics论文中使用的100个合成CC11群落的测序读段。其中： 454目录存放使用人类微生物组计划（Human Microbiome Project, HMP）454引物扩增得到的模拟454焦磷酸测序读段；illumina目录存放使用地球微生物组计划（Earth Microbiome Project, EMP）引物扩增得到的类MiSeq双端测序读段。两类目录均包含无误差模拟读段、带模拟误差的读段，以及一张映射文件（用于标注每条序列ID所属的群落，以及每条读段的"真实"来源序列）。 - CC11_targets.csv：适配DECARD工具的目标文件，可结合16S_SSU.tar.bz2中的筛选读段与自选引物序列重建CC11群落，可用于测试不同引物组合的效果。 - CC11_targets.tre：所有CC11群落所用全长16S序列的"真实"系统发育树，格式为Newick，可用于Phyloseq等工具计算群落间的真实双分量协方差分析（Double Principal Coordinate Analysis, DPCoA）或（加权）UniFrac成对距离。