Silva taxonomic training data formatted for DADA2 (Silva version 138.2)
Description
These DADA2-formatted training fasta files were derived from the Silva Project's version 138.2 release: https://www.arb-silva.de/
These fastas were generated by the following commands (using the dada2 R package version 1.35.4):
path <- "~/tax/Silva/v138_2"
fn.out.slv <- "~/Desktop/silva_nr99_v138.2_toGenus_trainset.fa.gz"
dada2:::makeTaxonomyFasta_SilvaNR(file.path(path, "SILVA_138.2_SSURef_NR99_tax_silva.fasta.gz"),
file.path(path, "tax_slv_ssu_138.2.txt"),
fn.out.slv)
fn.out.spc.slv <- "~/Desktop/silva_nr99_v138.2_toSpecies_trainset.fa.gz"
dada2:::makeTaxonomyFasta_SilvaNR(file.path(path, "SILVA_138.2_SSURef_NR99_tax_silva.fasta.gz"),
file.path(path, "tax_slv_ssu_138.2.txt"),
fn.out.spc.slv, include.species=TRUE)fn.out.aS.slv <- "~/Desktop/silva_v138.2_assignSpecies.fa.gz"
dada2:::makeSpeciesFasta_Silva("~/tax/silva/v138_2/SILVA_138.2_SSURef_tax_silva.fasta.gz",
fn.out.aS.slv)
Files
Files
(350.9 MB)
| Name | Size | Download all |
|---|---|---|
|
md5:1764e2a36b4500ccb1c7d5261948a414
|
140.0 MB | Download |
|
md5:e0455a1a7de820039d684aad2053e937
|
141.0 MB | Download |
|
md5:62fd939bd1aa9832d2089847f9f0b87d
|
69.9 MB | Download |
Additional details
Funding
- National Institutes of Health
- Quantitative Metagenomics and the Vaginal Microbiome of Preterm Birth R35GM133745
References
- Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucl. Acids Res. 41 (D1): D590-D596.
- Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nature methods. 2016 Jul;13(7):581-3.