CyanoSeq is published in the Journal of Phycology: https://doi.org/10.1111/jpy.13335
CyanoSeq is a curated database of cyanobacterial 16S rRNA sequences for taxonomic assignment of metagenomic/metabarcoding/amplicon reads. CyanoSeq is assembled from 16S rRNA sequences found within NCBI, with their taxonomies curated from cyanobacterial taxonomic literature as well as a systematic assessment of uncharacterized cyanobacterial sequences. When possible, the full length 16S rRNA sequences are provided, allowing use for several 16S rRNA primer sets to be used for metabarcoding, as well as full length 16S rRNA sequences for taxonomic assignment. The taxonomy of CyanoSeq is meant to reflect the current state of cyanobacterial taxonomy with curated clades of described and undescribed taxa. A provisional rank was given to those taxa that fell outside of the sensu stricto clade in an attempt to resolve polyphletic ranks. CyanoSeq does not aim to revise cyanobacterial taxonomy nor become a taxonomic authority, rather it serves as a starting point to identify and name monophyletic clades which do not belong to any established taxonomic rank and require revision. CyanoSeq currently contains 14458 cyanobacterial sequences and 123 chloroplast and bacterial sequences for use in classifying reads from metagenomic studies.
Two fastq.qz files are provdied for taxonomic assignment using the "assignTaxonomy" function in DADA2. Additional files are provided for QIIME2 and IdTaxa classifiers. These files have not been tested, please let me know if these work or not.
CyanoSeq_1.2_dada2.fastq.gz is the Cyanobacterial data bases which contains 14458 cyanobacterial sequences and 123 chloroplast and bacterial sequences and can be used with cyanobacterial specific primers (i.e., those described by Nübel et al., 1997)
CyanoSeq_1.1.2_SILVA138.1_dada2.fastq.gz is the cyanobacterial database merged with SILVA, current version 138.1, with the cyanobacterial sequences from SILVA removed and replaced with those curated here, and the Class “Cyanobacteriia” replaced with “Cyanophyceae” and order "Cyanobacteria" replaced with "Cyanobacteriota". This can be used general bacterial primers to fully understand the bacterial and cyanobacterial communities.
Leave a request or start a discussion here, or email me at flefler(at)ufl(dot)edu