Computational protocol: Autogenic succession and deterministic recovery following disturbance in soil bacterial communities

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Protocol publication

[…] cDNA obtained from 10 ng of total RNA was used for 16S rRNA gene transcript sequencing. A gene fragment of 460 bp flanking the V3 and V4 regions of the 16S rRNA gene was amplified using primers 341F and 806R. Sequencing of the amplicons was performed using MiSeq reagent kit v2 (500 cycles) on a MiSeq sequencer (Illumina Inc., San Diego, CA, U.S.A). Additional information regarding sequencing conditions and processing methods is provided in . Briefly, paired end reads were merged and trimmed using Biopieces (www.biopieces.org) and UPARSE. OTUs were clustered and their abundances were calculated using USEARCH. OTUs were chimera-checked with UCHIME against the Greengenes 2011 database. Singleton OTUs were removed. Following quality checking and trimming, we obtained 4 364 988 sequences with an average of 39 896 reads per sample (a range of 505 to 130 033 reads per sample). […]

Pipeline specifications

Software tools Biopieces, UPARSE, USEARCH, UCHIME
Databases Greengenes
Application 16S rRNA-seq analysis