A collection of tools useful for 16s rRNA sequencing (not comprehensive)
General tools
Unix environment
Scripting (Perl/Python/bash)
R
Read trimming (and adaptor removal)
Trimmomatic http://www.usadellab.org/cms/?page=trimmomatic
ConDeTri https://github.com/linneas/condetri
FASTX-Toolkit http://hannonlab.cshl.edu/fastx_toolkit/
cutadapt https://github.com/marcelm/cutadapt
BBDuk https://sourceforge.net/projects/bbmap/
Merge paired end reads
vsearch https://github.com/torognes/vsearch
usearch http://www.drive5.com/usearch/
PEAR https://sco.h-its.org/exelixis/web/software/pear/
FLASh http://ccb.jhu.edu/software/FLASH/
MeFiT https://github.com/nisheth/MeFiT
Quality filtering
vsearch https://github.com/torognes/vsearch
usearch http://www.drive5.com/usearch/
MeFiT https://github.com/nisheth/MeFiT
Chimera discovery
vsearch https://github.com/torognes/vsearch
usearch http://www.drive5.com/usearch/
Dereplication/OTU clustering/Taxonomic assignments
vsearch https://github.com/torognes/vsearch
usearch http://www.drive5.com/usearch/
mothur https://www.mothur.org/
QIIME2 https://qiime2.org/
Phylogenetic tree reconstruction
FastTree http://www.microbesonline.org/fasttree/
Downstream analysis (e.g. alpha/beta diversity, indicator species)
phyloseq http://joey711.github.io/phyloseq/
mothur https://www.mothur.org/
vegan https://cran.r-project.org/web/packages/vegan/index.html
indicspecies https://cran.r-project.org/web/packages/indicspecies/
DESeq2 http://bioconductor.org/packages/release/bioc/html/DESeq2.html
ALDEx2 https://bioconductor.org/packages/release/bioc/html/ALDEx2.html
QIIME2 https://qiime2.org/
metagenomeSeq http://cbcb.umd.edu/software/metagenomeSeq/
microbiome https://github.com/microbiome/microbiome/
Pipeline platforms (interactive)
mothur https://www.mothur.org/
QIIME2 https://qiime2.org/
MEGAN http://ab.inf.uni-tuebingen.de/software/megan6/