title: bacterial community35
design: Raw sequencing data were in FASTQ format. SINGLE-end reads were then preprocessed using Trimmomatic software to detect and cut off ambiguous bases (N). It also cut off low quality sequences with average quality score below 20 using sliding window trimming approach. After trimming, SINGLE-end reads were assembled using FLASH software. Parameters of assembly were: 10bp of minimal overlapping, 200bp of maximum overlapping and 20% of maximum mismatch rate. Sequences were performed further denoising as follows: reads with ambiguous, homologous sequences or below 200bp were abandoned. Reads with 75% of bases above Q20 were retained. Then, reads with chimera were detected and removed. These two steps were achieved using QIIME software (version 1.8.0).