Computational protocol: Changes in soil bacterial community structure as a result of incorporation of Brassica plants compared with continuous planting eggplant and chemical disinfection in greenhouses

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Protocol publication

[…] Demultiplex Raw fastq files were quality-filtered by QIIME (version 1.17).OTUs were clustered with a 97% similarity cutoff by UPARSE (version 7.1 http://drive5.com/uparse/) and chimeric sequences were identified and removed by UCHIME.The taxonomy of the 16S rRNA gene sequence was analyzed by an RDP Classifier (http://rdp.cme.msu.edu/) against the SILVA (SSU115)16S rRNA database using a confidence threshold of 70% [].Rarefaction data and Simpson, Shannon-Weaver and Chao indices were created using Mothur (Version 1.36.1) []. [...] All statistical analyses were performed using SPSS statistical software (IBM SPSS Statistics 19). Differences at the P ≤ 0.05 level was considered to be statistically significant. […]

Pipeline specifications

Software tools QIIME, UPARSE, UCHIME, RDP Classifier, mothur, SPSS
Applications Miscellaneous, 16S rRNA-seq analysis
Organisms Solanum melongena
Diseases Cystic Fibrosis, Movement Disorders