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CREST - Classification Resources for Environmnetal Sequence Tags, is a collection of software and databases for taxonomic classification of environmental marker genes from sequencing-based community profiling studies (also known as "meta-" + "-genomics", " -transcriptomics", "-barcoding"; "taxonomic-" or "phylogenetic-" profiling)). The program LCAClassifier is used used for classification of sequences aligned to the reference databases provided.
If you use CREST or the LCAClassifier in your research, please cite: Lanzén A , Jørgensen SL, Huson D, Gorfer M, Grindhaug SH, Jonassen I, Øvreås L, Urich T (2012) CREST - Classification Resources for Environmental Sequence Tags, PLoS ONE 7:e49334.
SilvaMod was derived by manual curation of the SILVA nr SSU Ref v128. It supports SSU sequences from bacteria and archaea (16S) as well as eukaryotes (18S), with a high level of manual curation and defined environmental clades.
Greengenes is an alternative reference database for classification of prokaryotic 16S, curated and maintained by The Greengenes Database Consortium. Release supported: May 2013
Unite seeks to maintain the cleanest possible copy of all public fungal ITS sequences. Third-party sequence annotation is supported, and everyone with the expertise to improve the sequence data and their annotation/metadata are welcome to participate in the annotation effort. Release supported: v7, 2016-01-31
amoA is a reference database for phylogenetic (not taxonomic) classification of ammonia monooxidase A (amoA) amplicons developed by Alves et al. (2018).
BOLD Barcode of Life Datasystems (BOLD) is a community resource including a reference database for COI (Mitochondrial Cytochrome Oxidase I) metabarcoding and barcoding. The partial version available here is from 2018 and has been adapted and curated for CREST, including standardizing rank structure and taxon names using the NCBI Taxonomy.