Metagenomic assemblies

Sample reads were co-assembled based on each sampling location using metaSPAdes v 3.11.1 with the following flags ‘-meta -t 16 --phred-offset 33 -m 500 -k 21,33,55,77,99,119’ and further filtered to a minimum scaffold length of 500 bp. Reads from samples and controls (i.e., extraction blank, filter blank, DI water blank) were mapped to co-assemblies using BWA-MEM. An approach similar to Dai et al.(Dai et al., 2020) was used to remove potential contaminant scaffolds.

基于各采样位点的样本测序读段，采用宏基因组拼接工具metaSPAdes v3.11.1进行共组装，所用命令行参数为‘-meta -t 16 --phred-offset 33 -m 500 -k 21,33,55,77,99,119’；随后对组装得到的序列进行过滤，仅保留长度不低于500 bp的scaffold（骨架序列）。使用BWA-MEM工具将样本与对照样本（即提取空白组、过滤空白组、去离子水空白组）的测序读段比对至上述共组装序列集。参考Dai等人（Dai et al., 2020）的研究方法，移除潜在的污染性骨架序列。