CCavallo_Thesis Appendix_NGS Bioinformatics pipeline 16S.Rmd

Bioinformatic workflow.This code will allow the user to clean and organise their DNA sample library and then calculate measures of taxon abundance for analysis. Important steps include: * Removing + samples with less than 100 target reads + Non-target sequences + Specific samples (e.g. those that did not meet thresholds for inclusion, like CT) * Producing group totals for higher taxonomic levels * Calculating the frequency of occurrence (FOO) and relative read abundance (RRA) of items in the dataset生物信息学工作流（Bioinformatic workflow）。本代码可协助用户完成DNA样本文库的清理与整理，并进一步计算分类群丰度指标以供分析使用。关键执行步骤如下： * 移除 + 目标读段数不足100的样本 + 非目标序列 + 未达到纳入阈值的特定样本（如循环阈值（CT）未达标的样本） * 生成高阶分类阶元的组总计数 * 计算数据集中各条目出现频率（frequency of occurrence, FOO）与相对读段丰度（relative read abundance, RRA）