Community assembly amplicon sequences, with pipeline to get asv table for "Spatial structure drives compositional convergence between nutrient environments in experimental microbial communities"

Community assembly amplicon sequences, with pipeline to get asv table for "Spatial structure drives compositional convergence between nutrient environments in experimental microbial communities"

compressed FASTA files for 16s amplicon sequences relating to two separate projects,  "Spatial structure drives compositional convergence between nutrient environments in experimental microbial communities" and "Habitat filtering leads to phylogenetic clustering in synthetic microbial communities". DADA22 pipeline is included, which pools all samples for better accuracy. A Julia script bioinfo.jl is then used to select only the samples relevant to spatial structure project.

All csv filenames are appended with "_q" indicating an increase in the stringency of quality filtering parameters (also increasing minimum hamming distance used in DADA2 algorithm to 5) to produce a taxa table with a sensible number of ASVs (given a known number of input strains) with each ASV uniquely aligning to an individual sequence from colony PCR of said input strains.

本数据集为群落组装扩增子序列，配套有用于生成《空间结构驱动实验微生物群落营养环境间组成趋同性》(Spatial structure drives compositional convergence between nutrient environments in experimental microbial communities)研究所需扩增子序列变异(Amplicon Sequence Variant, ASV)表的分析流程。数据集包含两项独立研究相关的16S扩增子序列压缩FASTA文件，分别对应上述空间结构研究，以及《生境过滤导致合成微生物群落发生系统发育聚类》(Habitat filtering leads to phylogenetic clustering in synthetic microbial communities)。本数据集附带DADA22分析流程，该流程通过合并所有样本以提升分析准确性；后续将通过Julia脚本bioinfo.jl筛选出仅与空间结构研究相关的样本。所有CSV文件名均附加后缀“_q”，该后缀代表质量过滤参数严格程度提升，同时将DADA22算法中使用的最小汉明距离调整为5，最终生成的分类群表中，扩增子序列变异(ASV)数量与已知输入菌株数相符，且每个ASV均可唯一比对至对应输入菌株的菌落PCR所得单条序列。