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  • Release information: SILVA 138. 1
    We decided to switch from an old version of UCLUST (1 0 50; reference to the UCLUST implementation in USEARCH) to a recent version of VSEARCH (2 13) which increases clustering performance and will, hopefully, allow us to provide a more stable Ref NR (in terms of reference sequences) in the future
  • protocols How-to-generate-USEARCH-compatible-SILVA138-fasta. md at . . .
    2 tanslate SILVA taxId to USEARCH compatible taxonomy Note: remove 1:N species to genus map vote strategy 3 remove Eukaryota clade and format taxon names protocols for bioinformatics data analysis Contribute to jameslz protocols development by creating an account on GitHub
  • SINTAX downloads - drive5
    Video talks on 16S data analysis posted URMAP ultra-fast read mapper posted (paper) ~20% of taxonomy annotations in SILVA and Greengenes are wrong Taxonomy prediction is <50% accurate for 16S V4 sequences 97% OTU threshold is wrong for species, should be 99% for full-length 16S, 100% V4
  • USEARCH - drive5
    USEARCH is a unique sequence analysis tool with thousands of users world-wide USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST USEARCH combines many different algorithms into a single package with outstanding documentation and support
  • Silva
    SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S 18S, SSU) and large subunit (23S 28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya) SILVA are the official databases of the software package ARB
  • Silva reference files - mothur
    Silva reference files If you use the SILVA reference files you should be aware of their dual-use license that covers Release 132 and earlier Release 138 2 The SILVA alignment is 50,000 columns long so that it can be compatible with 18S rRNA sequences as well as archaeal 16S rRNA sequences
  • Download - arb-silva. de
    SILVA provides comprehensive, quality checked and regularly updated databases of aligned small (16S 18S, SSU) and large subunit (23S 28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya)
  • silva_nr_v138_train_set_usearch_SINTAX_compatible. fa - figshare
    Usearch formatted silva v138 converted from dada2-format (from here: https: zenodo org record 3731176# XqsLVBNKhqU)
  • Silva 138. 1 prokaryotic SSU taxonomic training data formatted . . . - Zenodo
    These training fasta files are derived from the Silva Project's version 138 1 release and formatted for use with DADA2 These files are intended for use in classifying prokaryotic 16S sequencing data and are not appropriate for classifying eukaryotic ASVs





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