Greengenes2 unifies microbial data in a single reference tree
from contexts ‘Deblur_2021.09-Illumina-16S-V4-90nt-dd6875’, ‘Deblur_2021.09-Illumina-16S-V4-100nt-50b3a2’, ‘Deblur_2021.09-Illumina-16S-V4-125nt-92f954’, ‘Deblur_2021.09-Illumina-16S-V4-150nt-ac8c0b’, ‘Deblur_2021.09-Illumina-16S-V4-200nt-0b8b48’ and ‘Deblur_2021.09-Illumina-16S-V4-250nt-8b2bff’ and aligned them to the existing 16S alignment of sequences in WoL2 using UPP, setting the maximum alignment subset size to 200 .
The actual taxonomy decoration occurs on the backbone tree, which contains only full-length 16S records and does not contain ASVs. This is done as ASV placements are independent, do not modify the backbone and would substantially increase the computational resources required.
, we reduced the dimension of the tree by collapsing fragment multifurcations to single nodes, dropping the tree to 522,849 tips.A feature table for the 27,015 16S rRNA V4 90-nucleotide EMP samples was obtained from redbiom. The ASVs were filtered to the overlap of ASVs present in Greengenes2. Any feature with <1% relative abundance within a sample was removed. The feature table was then rarefied to 1,000 sequences per sample.
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