Metagenome sample from activated sludge A2 metagenome
In order to obtain the clean data for subsequent analysis, raw reads with > 40 low-quality bases (quality threshold value 38) or with > 10 ambiguous N bases were removed. In addition, the reads that shared an overlap of > 15 bases with the adapter were also removed.The clean data was assembled and analyzed with MEGAHIT software (version 1.0.4) to acquire scaffolds. The assembled scaffolds were then interrupted from N connections to acquire scaftigs without N. The clean data from all samples were aligned to each scaftig, respectively, with Bowtie2 software (version 2.2.4) to acquire the reads not used, which were combined and then were processed as described above for mixed assembly. Scaftigs less than 500 bp were filtered out.