dada2 taxa — dada2_taxa • micro4R

dada2 taxa

Usage

dada2_taxa(
  asvtable = NULL,
  train = NULL,
  species = NULL,
  chatty = TRUE,
  multi = FALSE,
  example = FALSE,
  ...
)

Arguments

asvtable: A file containging your sequences; most commonly the ASV table output from dada2.
train: Path to database that you'd like to use for taxonomic assignment.
species: OPTIONAL: path to database if you'd like to use assignSpecies() function
chatty: Set to FALSE for less text to print to screen
multi: Set to TRUE to use mutithreading where possible
example: Run example data. Default is FALSE
...: Allows passing of arguments to nested functions

Value

A table of taxonomic assigments

Examples

asvtable <- dada2_asvtable(where = "inst/extdata/f", logfile = FALSE)
#> [1] "Because you're running the example, any output files will go to a temporary directory, /tmp/Rtmpz0N6h9/dada2_out. To avoid cluttering your computer, this folder and its contents should all be deleted at the end of your R session."
#> [1] "Because you're running the example, any output files will go to a temporary directory, /tmp/Rtmpz0N6h9/dada2_out. To avoid cluttering your computer, this folder and its contents should all be deleted at the end of your R session."
#> Overwriting file:/tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5080-MS-1_307-ATAGTACC-ACGTCTCG_S307_L001_F_filt.fastq.gz
#> Overwriting file:/tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5080-MS-1_307-ATAGTACC-ACGTCTCG_S307_L001_R_filt.fastq.gz
#> Read in 50 paired-sequences, output 11 (22%) filtered paired-sequences.
#> Overwriting file:/tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5080-MS-1_313-GACATAGT-TCGACGAG_S313_L001_F_filt.fastq.gz
#> Overwriting file:/tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5080-MS-1_313-GACATAGT-TCGACGAG_S313_L001_R_filt.fastq.gz
#> Read in 50 paired-sequences, output 26 (52%) filtered paired-sequences.
#> Overwriting file:/tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5080-MS-1_328-GATCTACG-TCGACGAG_S328_L001_F_filt.fastq.gz
#> Overwriting file:/tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5080-MS-1_328-GATCTACG-TCGACGAG_S328_L001_R_filt.fastq.gz
#> Read in 50 paired-sequences, output 46 (92%) filtered paired-sequences.
#> Overwriting file:/tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5080-MS-1_339-ACTCACTG-GATCGTGT_S339_L001_F_filt.fastq.gz
#> Overwriting file:/tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5080-MS-1_339-ACTCACTG-GATCGTGT_S339_L001_R_filt.fastq.gz
#> Read in 50 paired-sequences, output 41 (82%) filtered paired-sequences.
#> Overwriting file:/tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5348-MS-1_162-ACGTGCGC-GGATATCT_S162_L001_F_filt.fastq.gz
#> Overwriting file:/tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5348-MS-1_162-ACGTGCGC-GGATATCT_S162_L001_R_filt.fastq.gz
#> Read in 50 paired-sequences, output 37 (74%) filtered paired-sequences.
#> Overwriting file:/tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5348-MS-1_297-GTCTGCTA-ACGTCTCG_S297_L001_F_filt.fastq.gz
#> Overwriting file:/tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5348-MS-1_297-GTCTGCTA-ACGTCTCG_S297_L001_R_filt.fastq.gz
#> Read in 50 paired-sequences, output 44 (88%) filtered paired-sequences.
#> Overwriting file:/tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5348-MS-1_381-TGCTCGTA-GTCAGATA_S381_L001_F_filt.fastq.gz
#> Overwriting file:/tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5348-MS-1_381-TGCTCGTA-GTCAGATA_S381_L001_R_filt.fastq.gz
#> Read in 50 paired-sequences, output 43 (86%) filtered paired-sequences.
#> 59520 total bases in 248 reads from 7 samples will be used for learning the error rates.
#> Initializing error rates to maximum possible estimate.
#> selfConsist step 1 .......
#>    selfConsist step 2
#> Convergence after  2  rounds.
#> 49600 total bases in 248 reads from 7 samples will be used for learning the error rates.
#> Initializing error rates to maximum possible estimate.
#> selfConsist step 1 .......
#>    selfConsist step 2
#> Convergence after  2  rounds.
#> Dereplicating sequence entries in Fastq file: /tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5080-MS-1_307-ATAGTACC-ACGTCTCG_S307_L001_F_filt.fastq.gz
#> Encountered 11 unique sequences from 11 total sequences read.
#> Dereplicating sequence entries in Fastq file: /tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5080-MS-1_313-GACATAGT-TCGACGAG_S313_L001_F_filt.fastq.gz
#> Encountered 25 unique sequences from 26 total sequences read.
#> Dereplicating sequence entries in Fastq file: /tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5080-MS-1_328-GATCTACG-TCGACGAG_S328_L001_F_filt.fastq.gz
#> Encountered 37 unique sequences from 46 total sequences read.
#> Dereplicating sequence entries in Fastq file: /tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5080-MS-1_339-ACTCACTG-GATCGTGT_S339_L001_F_filt.fastq.gz
#> Encountered 36 unique sequences from 41 total sequences read.
#> Dereplicating sequence entries in Fastq file: /tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5348-MS-1_162-ACGTGCGC-GGATATCT_S162_L001_F_filt.fastq.gz
#> Encountered 30 unique sequences from 37 total sequences read.
#> Dereplicating sequence entries in Fastq file: /tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5348-MS-1_297-GTCTGCTA-ACGTCTCG_S297_L001_F_filt.fastq.gz
#> Encountered 33 unique sequences from 44 total sequences read.
#> Dereplicating sequence entries in Fastq file: /tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5348-MS-1_381-TGCTCGTA-GTCAGATA_S381_L001_F_filt.fastq.gz
#> Encountered 36 unique sequences from 43 total sequences read.
#> Dereplicating sequence entries in Fastq file: /tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5080-MS-1_307-ATAGTACC-ACGTCTCG_S307_L001_R_filt.fastq.gz
#> Encountered 11 unique sequences from 11 total sequences read.
#> Dereplicating sequence entries in Fastq file: /tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5080-MS-1_313-GACATAGT-TCGACGAG_S313_L001_R_filt.fastq.gz
#> Encountered 23 unique sequences from 26 total sequences read.
#> Dereplicating sequence entries in Fastq file: /tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5080-MS-1_328-GATCTACG-TCGACGAG_S328_L001_R_filt.fastq.gz
#> Encountered 35 unique sequences from 46 total sequences read.
#> Dereplicating sequence entries in Fastq file: /tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5080-MS-1_339-ACTCACTG-GATCGTGT_S339_L001_R_filt.fastq.gz
#> Encountered 35 unique sequences from 41 total sequences read.
#> Dereplicating sequence entries in Fastq file: /tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5348-MS-1_162-ACGTGCGC-GGATATCT_S162_L001_R_filt.fastq.gz
#> Encountered 31 unique sequences from 37 total sequences read.
#> Dereplicating sequence entries in Fastq file: /tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5348-MS-1_297-GTCTGCTA-ACGTCTCG_S297_L001_R_filt.fastq.gz
#> Encountered 32 unique sequences from 44 total sequences read.
#> Dereplicating sequence entries in Fastq file: /tmp/Rtmpz0N6h9/dada2_out/filtered/SAMPLED_5348-MS-1_381-TGCTCGTA-GTCAGATA_S381_L001_R_filt.fastq.gz
#> Encountered 37 unique sequences from 43 total sequences read.
#> Sample 1 - 11 reads in 11 unique sequences.
#> Sample 2 - 26 reads in 25 unique sequences.
#> Sample 3 - 46 reads in 37 unique sequences.
#> Sample 4 - 41 reads in 36 unique sequences.
#> Sample 5 - 37 reads in 30 unique sequences.
#> Sample 6 - 44 reads in 33 unique sequences.
#> Sample 7 - 43 reads in 36 unique sequences.
#> Sample 1 - 11 reads in 11 unique sequences.
#> Sample 2 - 26 reads in 23 unique sequences.
#> Sample 3 - 46 reads in 35 unique sequences.
#> Sample 4 - 41 reads in 35 unique sequences.
#> Sample 5 - 37 reads in 31 unique sequences.
#> Sample 6 - 44 reads in 32 unique sequences.
#> Sample 7 - 43 reads in 37 unique sequences.
#> 0 paired-reads (in 0 unique pairings) successfully merged out of 1 (in 1 pairings) input.
#> 0 paired-reads (in 0 unique pairings) successfully merged out of 10 (in 1 pairings) input.
#> 44 paired-reads (in 1 unique pairings) successfully merged out of 44 (in 1 pairings) input.
#> 37 paired-reads (in 2 unique pairings) successfully merged out of 37 (in 2 pairings) input.
#> 28 paired-reads (in 3 unique pairings) successfully merged out of 28 (in 3 pairings) input.
#> 41 paired-reads (in 2 unique pairings) successfully merged out of 41 (in 2 pairings) input.
#> 0 paired-reads (in 0 unique pairings) successfully merged out of 31 (in 3 pairings) input.
#> Identified 0 bimeras out of 6 input sequences.
train <- "inst/extdata/db/EXAMPLE_silva_nr99_v138.2_toGenus_trainset.fa.gz"
species <- "inst/extdata/db/EXAMPLE_silva_v138.2_assignSpecies.fa.gz"
dada2_taxa(asvtable = asvtable, train = train, species = species)
#> [1] "You're using the provided micro4R EXAMPLE reference databases. These are extremely tiny and unrealistic and meant only for testing and demonstrating purposes. DO NOT use them with your real data."
#> Finished processing reference fasta.
#>                                                                                                                                                                                                                                                                Kingdom   
#> TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGG  "Bacteria"
#> TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGG  "Bacteria"
#> TACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGGGCTCGTAGGTGGTTTGTCGCGTCGTCTGTGAAATTCTGGGGCTTAACTCCGGGCGTGCAGGCGATACGGGCATAACTTGAGTGCTGTAGGGGTAACTGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTTACTGGGCAGTTACTGACGCTGAGGAGCGAAAGCATGGGTAGCGAACAGG "Bacteria"
#> TACGTAGGGTGCAAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCACGTCGTCTGTGAAATTCCACAGCTTAACTGTGGGCGTGCAGGCGATACGGGCTGACTTGAGTACTGTAGGGGTAACTGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTTACTGGGCAGTTACTGACGCTGAGGAGCGAAAGCATGGGTAGCAAACAGG  "Bacteria"
#> TACGTAGGTGACAAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAGCGCAGGCGGTCTGTTTAGTCTAATGTGAAAGCCCACGGCTTAACCGTGGAACGGCATTGGAAACTGACAGACTTGAATGTAGAAGAGGAAAATGGAATTCCAAGTGTAGCGGTGGAATGCGTAGATATTTGGAGGAACACCAGTGGCGAAGGCGATTTTCTGGTCTAACATTGACGCTGAGGCTCGAAAGCGTGGGGAGCGAACAGG  "Bacteria"
#> TACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTAGATAAGTCTGAAGTTAAAGGCTGTGGCTTAACCATAGTACGCTTTGGAAACTGTTTAACTTGAGTGCAAGAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGCTTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG   "Bacteria"
#>                                                                                                                                                                                                                                                                Phylum          
#> TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGG  "Bacillota"     
#> TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGG  "Pseudomonadota"
#> TACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGGGCTCGTAGGTGGTTTGTCGCGTCGTCTGTGAAATTCTGGGGCTTAACTCCGGGCGTGCAGGCGATACGGGCATAACTTGAGTGCTGTAGGGGTAACTGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTTACTGGGCAGTTACTGACGCTGAGGAGCGAAAGCATGGGTAGCGAACAGG "Actinomycetota"
#> TACGTAGGGTGCAAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCACGTCGTCTGTGAAATTCCACAGCTTAACTGTGGGCGTGCAGGCGATACGGGCTGACTTGAGTACTGTAGGGGTAACTGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTTACTGGGCAGTTACTGACGCTGAGGAGCGAAAGCATGGGTAGCAAACAGG  "Actinomycetota"
#> TACGTAGGTGACAAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAGCGCAGGCGGTCTGTTTAGTCTAATGTGAAAGCCCACGGCTTAACCGTGGAACGGCATTGGAAACTGACAGACTTGAATGTAGAAGAGGAAAATGGAATTCCAAGTGTAGCGGTGGAATGCGTAGATATTTGGAGGAACACCAGTGGCGAAGGCGATTTTCTGGTCTAACATTGACGCTGAGGCTCGAAAGCGTGGGGAGCGAACAGG  "Bacillota"     
#> TACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTAGATAAGTCTGAAGTTAAAGGCTGTGGCTTAACCATAGTACGCTTTGGAAACTGTTTAACTTGAGTGCAAGAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGCTTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG   "Bacillota"     
#>                                                                                                                                                                                                                                                                Class                
#> TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGG  "Bacilli"            
#> TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGG  "Gammaproteobacteria"
#> TACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGGGCTCGTAGGTGGTTTGTCGCGTCGTCTGTGAAATTCTGGGGCTTAACTCCGGGCGTGCAGGCGATACGGGCATAACTTGAGTGCTGTAGGGGTAACTGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTTACTGGGCAGTTACTGACGCTGAGGAGCGAAAGCATGGGTAGCGAACAGG "Actinobacteria"     
#> TACGTAGGGTGCAAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCACGTCGTCTGTGAAATTCCACAGCTTAACTGTGGGCGTGCAGGCGATACGGGCTGACTTGAGTACTGTAGGGGTAACTGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTTACTGGGCAGTTACTGACGCTGAGGAGCGAAAGCATGGGTAGCAAACAGG  "Actinobacteria"     
#> TACGTAGGTGACAAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAGCGCAGGCGGTCTGTTTAGTCTAATGTGAAAGCCCACGGCTTAACCGTGGAACGGCATTGGAAACTGACAGACTTGAATGTAGAAGAGGAAAATGGAATTCCAAGTGTAGCGGTGGAATGCGTAGATATTTGGAGGAACACCAGTGGCGAAGGCGATTTTCTGGTCTAACATTGACGCTGAGGCTCGAAAGCGTGGGGAGCGAACAGG  "Bacilli"            
#> TACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTAGATAAGTCTGAAGTTAAAGGCTGTGGCTTAACCATAGTACGCTTTGGAAACTGTTTAACTTGAGTGCAAGAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGCTTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG   "Bacilli"            
#>                                                                                                                                                                                                                                                                Order             
#> TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGG  "Staphylococcales"
#> TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGG  "Enterobacterales"
#> TACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGGGCTCGTAGGTGGTTTGTCGCGTCGTCTGTGAAATTCTGGGGCTTAACTCCGGGCGTGCAGGCGATACGGGCATAACTTGAGTGCTGTAGGGGTAACTGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTTACTGGGCAGTTACTGACGCTGAGGAGCGAAAGCATGGGTAGCGAACAGG "Mycobacteriales" 
#> TACGTAGGGTGCAAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCACGTCGTCTGTGAAATTCCACAGCTTAACTGTGGGCGTGCAGGCGATACGGGCTGACTTGAGTACTGTAGGGGTAACTGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTTACTGGGCAGTTACTGACGCTGAGGAGCGAAAGCATGGGTAGCAAACAGG  "Mycobacteriales" 
#> TACGTAGGTGACAAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAGCGCAGGCGGTCTGTTTAGTCTAATGTGAAAGCCCACGGCTTAACCGTGGAACGGCATTGGAAACTGACAGACTTGAATGTAGAAGAGGAAAATGGAATTCCAAGTGTAGCGGTGGAATGCGTAGATATTTGGAGGAACACCAGTGGCGAAGGCGATTTTCTGGTCTAACATTGACGCTGAGGCTCGAAAGCGTGGGGAGCGAACAGG  "Lactobacillales" 
#> TACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTAGATAAGTCTGAAGTTAAAGGCTGTGGCTTAACCATAGTACGCTTTGGAAACTGTTTAACTTGAGTGCAAGAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGCTTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG   "Lactobacillales" 
#>                                                                                                                                                                                                                                                                Family              
#> TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGG  "Staphylococcaceae" 
#> TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGG  "Enterobacteriaceae"
#> TACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGGGCTCGTAGGTGGTTTGTCGCGTCGTCTGTGAAATTCTGGGGCTTAACTCCGGGCGTGCAGGCGATACGGGCATAACTTGAGTGCTGTAGGGGTAACTGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTTACTGGGCAGTTACTGACGCTGAGGAGCGAAAGCATGGGTAGCGAACAGG "Corynebacteriaceae"
#> TACGTAGGGTGCAAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCACGTCGTCTGTGAAATTCCACAGCTTAACTGTGGGCGTGCAGGCGATACGGGCTGACTTGAGTACTGTAGGGGTAACTGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTTACTGGGCAGTTACTGACGCTGAGGAGCGAAAGCATGGGTAGCAAACAGG  "Corynebacteriaceae"
#> TACGTAGGTGACAAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAGCGCAGGCGGTCTGTTTAGTCTAATGTGAAAGCCCACGGCTTAACCGTGGAACGGCATTGGAAACTGACAGACTTGAATGTAGAAGAGGAAAATGGAATTCCAAGTGTAGCGGTGGAATGCGTAGATATTTGGAGGAACACCAGTGGCGAAGGCGATTTTCTGGTCTAACATTGACGCTGAGGCTCGAAAGCGTGGGGAGCGAACAGG  "Carnobacteriaceae" 
#> TACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTAGATAAGTCTGAAGTTAAAGGCTGTGGCTTAACCATAGTACGCTTTGGAAACTGTTTAACTTGAGTGCAAGAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGCTTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG   "Streptococcaceae"  
#>                                                                                                                                                                                                                                                                Genus            
#> TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGG  "Staphylococcus" 
#> TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGG  "Klebsiella"     
#> TACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGGGCTCGTAGGTGGTTTGTCGCGTCGTCTGTGAAATTCTGGGGCTTAACTCCGGGCGTGCAGGCGATACGGGCATAACTTGAGTGCTGTAGGGGTAACTGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTTACTGGGCAGTTACTGACGCTGAGGAGCGAAAGCATGGGTAGCGAACAGG "Corynebacterium"
#> TACGTAGGGTGCAAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCACGTCGTCTGTGAAATTCCACAGCTTAACTGTGGGCGTGCAGGCGATACGGGCTGACTTGAGTACTGTAGGGGTAACTGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTTACTGGGCAGTTACTGACGCTGAGGAGCGAAAGCATGGGTAGCAAACAGG  "Corynebacterium"
#> TACGTAGGTGACAAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAGCGCAGGCGGTCTGTTTAGTCTAATGTGAAAGCCCACGGCTTAACCGTGGAACGGCATTGGAAACTGACAGACTTGAATGTAGAAGAGGAAAATGGAATTCCAAGTGTAGCGGTGGAATGCGTAGATATTTGGAGGAACACCAGTGGCGAAGGCGATTTTCTGGTCTAACATTGACGCTGAGGCTCGAAAGCGTGGGGAGCGAACAGG  "Dolosigranulum" 
#> TACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTAGATAAGTCTGAAGTTAAAGGCTGTGGCTTAACCATAGTACGCTTTGGAAACTGTTTAACTTGAGTGCAAGAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGCTTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG   "Streptococcus"