10.28.22 Greengenes2 ----------- Welcome to the Greengenes2 FTP (http://ftp.microbio.me/greengenes_release/), the official source for Greengenes2 releases. Construction ------------ Greengenes2 is based on the whole genome Web of Life phylogeny. The phylogeny is then updated with full length 16S records from GTDB, the Living Tree Project, SILVA, and Karst et al Nature Methods 2021 using a novel method called uDance. Following update, approximately 20,000,000 16S V4 ASVs from Qiita are inserted into the tree using DEPP. The result of this process is a single phylogeny, and taxonomy, that is suitable for both shotgun metagenomic studies, as well as 16S rRNA studies. How to use? ----------- The primary supported method for using Greengenes2 is through its QIIME 2 plugin. The plugin can be obtained from https://github.com/biocore/q2-greengenes2. Files ----- * 00README This file * 00CHANGELOG Details on changes about the resource between versions * 00LICENSE The BSD-3 license these files are released under * 2022.10.backbone.full-length.fna.qza All the full length 16S sequences in the backbone of the tree * 2022.10.backbone.tax.qza Taxonomy information for the backbone * 2022.10.backbone.v4.fna.qza In silico extracted V4 sequences from the backbone based on the EMP 16S primers * 2022.10.backbone.v4.nb.qza * 2022.10.backbone.full-length.nb.qza Naive Bayes classifier trained on the V4 region, and separately, the full length 16S from the backbone sequences. * 2022.10.backbone.sepp-reference.qza A SEPP compatible reference for 16S rRNA fragment insertion. * 2022.10.phylogeny.asv.nwk * 2022.10.phylogeny.asv.nwk.qza * 2022.10.phylogeny.id.nwk * 2022.10.phylogeny.id.nwk.qza * 2022.10.phylogeny.md5.nwk * 2022.10.phylogeny.md5.nwk.qza The full phylogeny. Fragments are expressed as ASVs, simple IDs, or MD5s as tips. We also provided as a QIIME 2 QZA files. * 2022.10.seqs.fna.gz * 2022.10.seqs.fna.qza All sequences used in the construction of the tree * 2022.10.taxonomy.asv.nwk * 2022.10.taxonomy.asv.nwk.qza * 2022.10.taxonomy.asv.tsv.gz * 2022.10.taxonomy.asv.tsv.qza * 2022.10.taxonomy.id.nwk * 2022.10.taxonomy.id.nwk.qza * 2022.10.taxonomy.id.tsv.gz * 2022.10.taxonomy.id.tsv.qza * 2022.10.taxonomy.md5.nwk * 2022.10.taxonomy.md5.nwk.qza * 2022.10.taxonomy.md5.tsv.gz * 2022.10.taxonomy.md5.tsv.qza The full taxonomic records for the database. Fragments are expressed as ASVs, simple IDs or MD5s. We also provide QIIME 2 QZA files. The taxonomy is expressed both in tab delimited form as well as Newick Citing ------ If you use Greengenes2, please cite McDonald et al Nature Biotechnology 2023 (https://www.nature.com/articles/s41587-023-01845-1). Contact ------- Daniel McDonald damcdonald@ucsd.edu Edits ----- * 2024.09.06 - added 2022.10.backbone.sepp-reference.qza - updated contact email