PyNAST

[…] of smrt portal version 2.7 (pacific biosciences). high-quality sequences were extracted using the quantitative insights into microbial ecology (qiime) package (version 1.7) and aligned by pynast and uclust under 100% clustering of sequence identity to obtain representative sequences. the unique sequence set was classified into otus under 98.6% threshold identity using uclust. […]

[…] 2.0) method () with a minimum identity of 97%. taxonomy was assigned using uclust (version 1.2.22) () with the greengenes database as reference (version 13.8) and sequences were aligned using pynast (version 1.2.2) (). otu’s identified in less than 0.1% of the reads were removed as well as reads identified as chloroplast or mitochondria. archaea were not filtered out. picrust (version […]

[…] obtained through each step is reported in table . high-quality amplicon reads were subsequently analysed by the qiime pipeline, aligning them against the silva database (v119) by means of the pynast aligner using the open-reference strategy and clustering them at 97% of identity. the chimeraslayer tool was used to assess the presence of chimeric sequences, which were not found […]

[…] taxonomic units (otus) were generated for the remaining sequences based on a 97% sequence similarity with the uclust method (). the representative sequences were picked for each otu, aligned using pynast (), and assigned into taxonomic groups against the greengenes database v.13.8 (). construction of phylogenic tree was conducted with the program fasttree (). the otus assigned into archaea, […]

[…] abundant sequence in each otu. representative sequences (at 97% similarity) were then classified taxonomically using ribosomal database project (rdp) classifier 2.0.1. the otus were aligned using pynast with a minimum alignment length of 150 bp and a minimum percent identity of 75%. after alignment, ph lane mask (http://greengenes.lbl.gov/) was conducted to screen out the hypervariable […]

[…] 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. […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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). […]