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15 de jun. de 2018 · We finally compared the performance of the hand-curated Metaxa2 SSU rRNA database that is bundled with the software to SSU rRNA databases built by metaxa2_dbb from the sequences in SILVA release 111 and 128 (Quast et al., 2013).
- Johan Bengtsson-Palme, Johan Bengtsson-Palme, Rodney T Richardson, Marco Meola, Christian Wurzbacher...
- 2018
15 de jun. de 2018 · We tried two approaches: Metaxa2 [45] [46][47] coupled with the SILVA 132 SSU database [48,49] and MetaPhlAn3 [50,51], which uses a collection of marker genes. The taxonomic resolution...
26 de ago. de 2023 · Evaluations of reference libraries identified the SILVA and RefSeq/Kraken 2 Standard libraries as superior in accuracy compared to Greengenes. These findings support PathoScope and Kraken 2 as...
19 de oct. de 2017 · Greengenes is a 16S/Archaea database and SILVA is a 16S/18S/Archaea database. SILVA also has 23S/28S databases but I'm not sure if those are in a QIIME-compatible format. You can find a list of QIIME-compatible reference databases on the data resources page.
We finally compared the performance of the hand-curated Metaxa2 SSU rRNA database that is bundled with the software to SSU rRNA databases built by metaxa2_dbb from the sequences in SILVA release 111 and 128 (Quast et al., 2013).
14 de mar. de 2017 · The four taxonomies, SILVA, RDP, Greengenes and NCBI, commonly used for metagenomic analyses are compared in detail (Venn diagrams on the left) and then union of them (labeled ALL) is compared against OTT (Venn diagrams on the right).
underlying databases. The basis of the Metaxa2 databases is the SILVA reference release 111 and Mitozoa release 10. From this data, we have created a curated reference database, in large part by automated means, but also using extensive manual curation and cross-checking in GreenGenes, CRW and GenBank.
