/repromicrobiome2021

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Protocol settings

uclust refers to the default version that comes with qiime1 (1.2.22q); in all cases vsearch 2.15.2 was used instead of USEARCH61.

algorithm database pipeline settings snakefile strand rev folder
uclust (default settings) Greengenes 13.8 qiime1_settings.txt Snakefile no uclust_gg138_def
uclust Greengenes 13.8 otu_SILVA_settings.txt Snakefile yes uclust_gg138
uclust Greengenes 13.8 otu_SILVA_settings.txt Snakefile no uclust_gg138_norev
uclust (default settings) SILVA 119 otu_SILVA_settings.txt Snakefile no uclust_silva119_def
uclust SILVA 119 otu_SILVA_settings.txt Snakefile no uclust_silva119_norev
uclust SILVA 119 otu_SILVA_settings.txt Snakefile yes uclust_silva119_rev
uclust SILVA 132 otu_SILVA_settings.txt Snakefile no uclust_silva132_norev
uclust SILVA 132 otu_SILVA_settings.txt Snakefile yes uclust_silva132_rev
usearch61 SILVA 119 otu_SILVA_settings.txt Snakefile no usearch61_silva119_norev
usearch61 SILVA 119 otu_SILVA_settings.txt Snakefile yes usearch61_silva119_rev
usearch61 SILVA 132 otu_SILVA_settings.txt Snakefile no usearch61_silva132_norev
usearch61 SILVA 132 otu_SILVA_settings.txt Snakefile yes usearch61_silva132_rev