Alfalfa microbe
Raw fastq files were demultiplexed, quality-filtered by Trimmomatic, and merged by FLASH with the following criteria: (a) the reads were truncated at any site receiving an average quality score <20 over a 50 bp sliding window; (b) primers were exactly matched allowing 2 nucleotide mismatching, and reads containing ambiguous bases were removed; (c) sequences whose overlap was longer than 10 bp were merged according to their overlap.