Processing of Illumina MiSeq-generated nifH amplicons from boreal forest moss samples - output after FunGene, CART models and chimera removal

A portion of the nifH (nitrogenase) gene was amplified from twelve samples of boreal forest moss stems (Pleurozium schreberi) from Sweden, using degenerate primers IGK3 and DVV. Sequencing was carried out using the Illumina MiSeq platform, paired-end 300 bp kit. Bioinformatic processing included the RDP FunGene pipeline and a classification and regressions trees (CART) model (Frank et al. 2016, Environ Microbiol Rep 8:905-916). Output from key steps is available here. Raw data are available on NCBI's SRA, accession numbers SRR5366534-SRR5366545.

研究人员从瑞典的12份北方森林赤茎藓（Pleurozium schreberi）茎秆样本中，利用简并引物IGK3与DVV扩增得到固氮酶（nitrogenase）基因nifH的一段序列。测序工作采用Illumina MiSeq平台及配对末端300 bp测序试剂盒完成。生物信息学处理流程包含RDP FunGene分析管线以及分类与回归树（CART）模型（Frank等，2016，Environ Microbiol Rep 8:905-916）。关键分析步骤的输出结果可在此处获取。原始数据已上传至NCBI的序列读取档案（SRA），登录号为SRR5366534至SRR5366545。