Database of 16S sequences from SILVA (r114), filtered, curated and annotated to be used easily by programs of taxonomic assignments

<p>The database used for the taxonomic assignment of reads generally comes from the SILVA database (http://www.arb-silva.de/). The logic behind this&nbsp;database is to use the&nbsp;information from the best one to the worst one. This is why the curated database was splitted in two parts : the [C] sequences for Complete sequences in&nbsp;terms of taxonomy, and the [I] and [E] sequences, for Incomplete and Environmental sequences.</p> <p>Each sequence included into the database must have a specific format summarizing&nbsp;all needed information (example below):<br> &gt;[I]AACY020336309;Archaea(superkingdom);Euryarchaeota(phylum);Thermoplasmata(class);Thermoplasmatales(order);Marine_Group_II(no_rank);;marine_metagenome</p> <p>This sequence is an incomplete one ([I]), with a specific accession number from NCBI or SILVA, or another database (AACY020336309). Then, all taxonomic data is&nbsp;separated using &#39;;&#39; characters, for each considered level (superkingdom, phylum,&nbsp;<br> class, order, family, and genus). The species name is the last one and separated by two &#39;;&#39; characters from the rest of the descriptive line. Finally, the descriptive line must not contain specific characters like spaces. If one or several levels are unknown, this is indicated by &#39;no_rank&#39;.</p> <p>Another example here for [C] sequences:<br> &gt;[C]AAAK03000010;Bacteria(superkingdom);Firmicutes(phylum);Bacilli(class);Lactobacillales(order);Enterococcaceae(family);Enterococcus(genus);;Enterococcus_faecium_DO<br> This sequence is a complete one ([C]), with a specific accession number from NCBI or SILVA, or another database (AACY020187844). Then, all taxonomic data is&nbsp;separated using &#39;;&#39; characters, for each considered level (superkingdom, phylum,&nbsp;<br> class, order, family, and genus). The species is the last one and separated by two &#39;;&#39; characters from the rest of the descriptive line. Complete sequences&nbsp;must have six levels of information (superkingdom, phylum, class, order, family, and genus). If it is not the case, the sequence will be considered as Incomplete ([I]) (between three and five levels), or Environmental ([E]) (with only the superkingdom and the phylum levels).</p> <p>Another example here for [E] sequences:<br> &gt;[E]U59968;Archaea(superkingdom);Thaumarchaeota(phylum);Soil_Crenarchaeotic_Group(SCG)(no_rank);;uncultured_crenarchaeote<br> This sequence is a environmental one ([E]), with a specific accession number from NCBI or SILVA, or another database (U59968). Then, all taxonomic data is&nbsp;separated using &#39;;&#39; characters, for each considered level (superkingdom, phylum,&nbsp;class, order, family, and genus). The species is the last one and separated by two &#39;;&#39; characters from the rest of the descriptive line. Complete sequences&nbsp;<br> must have six levels of information (superkingdom, phylum, class, order, family, and genus). If it is not the case, the sequence will be considered as Incomplete ([I]) (between three and five levels), or Environmental ([E]) (with only the superkingdom and the phylum levels).</p> <p>More details on the steps defined to clean and define this new database can be available on demand (sebastien.terrat@inra.fr).</p>