DADA2 formatted eHOMD 16S rRNA gene sequences databse
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下载链接：
https://zenodo.org/record/7380291
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资源简介：
eHOMD Refseq database (V15.22) formated to be used with dada2 i.e., dada2::assignTaxonomy(seqs, "eHOMD_RefSeq_dada2_V15.22.fasta.gz" ) and dada2::addSpecies(taxa, "eHOMD_RefSeq_dada2_assign_species_V15.22.fasta.gz", verbose=TRUE)
Alternatively, you could use the metabaRpipe R package to directly update the taxonomy of a phyloseq object see: https://github.com/fconstancias/metabaRpipe#2-addingreplacing-taxonomical-table-in-a-phyloseq-object
Example below:
source("https://raw.githubusercontent.com/fconstancias/metabaRpipe-source/master/Rscripts/functions.R")
readRDS("dada2/phyloseq.RDS") %>%
phyloseq_dada2_tax(physeq = .,
threshold = 60,
db ="~/metabaRpipe/databases/eHOMD_RefSeq_dada2_V15.22.fasta.gz",
db_species ="~/metabaRpipe/databases/eHOMD_RefSeq_dada2_assign_species_V15.22.fasta.gz",
nthreads = 2,
full_return = FALSE) -> physeq_eHOMD_tax
创建时间：
2022-12-02
