PyNAST

[…] of lower than 20 were removed. Chimeric sequences were checked and removed using USEARCH version 6.1.544 (). The remaining high-quality reads were clustered into operational taxonomic units (OTUs) by PyNAST () with a 97% sequence identity threshold against the Greengenes core set database version 13.8 (). The generated biome table was normalized using an equal subsampling size of 2,938 sequences. […]

[…] For quality filtering, QIIME default parameters were used, with a minimun Phred quality score <20 and ambiguous nucleotides were removed. Sequence alignment was made using Greengenes database [] and PyNast alignment algorithm []. UCLUST software [] was used to assign similar sequences to operational taxonomic units (OTUs) by clustering sequences based on a 97% similarity threshold. The taxonomic […]

[…] _novo. As part of the pick_open_reference_otus.py workflow, representative sequences from each OTU were selected and aligned against the Greengenes database gg_13_8 preclustered at 85% identity using PyNAST [] and used to build a tree using FastTree []. The OTU matching to chloroplasts of plant origin (“Streptophyta”) based on Greengenes taxonomic classification was manually removed. To improve ta […]

[…] remaining reads were clustered into Operational Taxonomic Units (OTUs) at 97% similarity using uclust. Representative sequences were aligned against the Silva reference alignment (release 108,) using PyNAST and identified using the RDP Classifier. Rare OTUs (i.e. singletons and doubletons) were discarded, resulting in 1380 OTUs represented by ≥3 reads (see Supplementary Table  for details). All re […]

[…] a similarity threshold of 97% (roughly corresponding to species-level OTUs). Representative sequences from the OTUs were aligned to a pre-aligned database of sequences (the Greengenes core set) using PyNAST with quality thresholds set with a minimum sequence length of 150 nucleotides and a minimum percent identity of 75%. PyNAST alignment failures were investigated by blasting all sequences that f […]

[…] using the SILVA 128 database (99% identity level), using BLAST. Sequences classified as chloroplasts were removed from the final table, and samples were rarefied to a depth of 3,748 and aligned with Pynast (). Uninformative base positions based on the default lane mask were removed, and this alignment was used to generate a phylogeny by using the FastTree algorithm (). Alpha and beta diversity me […]