dada2 workflow to generate ASV table
dada2_asvtable.Rddada2 workflow to generate ASV table
Usage
dada2_asvtable(
where = NULL,
patternF = "_R1_001.fastq.gz",
patternR = "_R2_001.fastq.gz",
multi = FALSE,
chatty = TRUE,
logfile = TRUE,
...
)Arguments
- where
Path to your fastq files. Run
dada2_asvtable(path = "example")if you want to run the example data.- patternF
Pattern of the forward/R1 reads. Default is Illumina standard.
- patternR
Pattern of the reverse/R2 reads. Default is Illumina standard
- multi
Should multithreading be done? Can use this to set to TRUE or FALSE for entire wrapper.
- chatty
How chatty should code be? Default is TRUE, but set to FALSE if you don't want so much text going to the console.
- logfile
Write a logfile to user's computer. Default is TRUE
- ...
Allows passing of arguments to nested functions
Examples
dada2_asvtable("example", 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."
#> Creating output directory: /tmp/Rtmpz0N6h9/dada2_out/filtered
#> Read in 50 paired-sequences, output 11 (22%) filtered paired-sequences.
#> Read in 50 paired-sequences, output 26 (52%) filtered paired-sequences.
#> Read in 50 paired-sequences, output 46 (92%) filtered paired-sequences.
#> Read in 50 paired-sequences, output 41 (82%) filtered paired-sequences.
#> Read in 50 paired-sequences, output 37 (74%) filtered paired-sequences.
#> Read in 50 paired-sequences, output 44 (88%) filtered paired-sequences.
#> 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.
#> TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGG
#> SAMPLED_5080-MS-1_307-ATAGTACC-ACGTCTCG_S307_L001 0
#> SAMPLED_5080-MS-1_313-GACATAGT-TCGACGAG_S313_L001 0
#> SAMPLED_5080-MS-1_328-GATCTACG-TCGACGAG_S328_L001 44
#> SAMPLED_5080-MS-1_339-ACTCACTG-GATCGTGT_S339_L001 24
#> SAMPLED_5348-MS-1_162-ACGTGCGC-GGATATCT_S162_L001 0
#> SAMPLED_5348-MS-1_297-GTCTGCTA-ACGTCTCG_S297_L001 0
#> SAMPLED_5348-MS-1_381-TGCTCGTA-GTCAGATA_S381_L001 0
#> TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGG
#> SAMPLED_5080-MS-1_307-ATAGTACC-ACGTCTCG_S307_L001 0
#> SAMPLED_5080-MS-1_313-GACATAGT-TCGACGAG_S313_L001 0
#> SAMPLED_5080-MS-1_328-GATCTACG-TCGACGAG_S328_L001 0
#> SAMPLED_5080-MS-1_339-ACTCACTG-GATCGTGT_S339_L001 0
#> SAMPLED_5348-MS-1_162-ACGTGCGC-GGATATCT_S162_L001 0
#> SAMPLED_5348-MS-1_297-GTCTGCTA-ACGTCTCG_S297_L001 35
#> SAMPLED_5348-MS-1_381-TGCTCGTA-GTCAGATA_S381_L001 0
#> TACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGGGCTCGTAGGTGGTTTGTCGCGTCGTCTGTGAAATTCTGGGGCTTAACTCCGGGCGTGCAGGCGATACGGGCATAACTTGAGTGCTGTAGGGGTAACTGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTTACTGGGCAGTTACTGACGCTGAGGAGCGAAAGCATGGGTAGCGAACAGG
#> SAMPLED_5080-MS-1_307-ATAGTACC-ACGTCTCG_S307_L001 0
#> SAMPLED_5080-MS-1_313-GACATAGT-TCGACGAG_S313_L001 0
#> SAMPLED_5080-MS-1_328-GATCTACG-TCGACGAG_S328_L001 0
#> SAMPLED_5080-MS-1_339-ACTCACTG-GATCGTGT_S339_L001 0
#> SAMPLED_5348-MS-1_162-ACGTGCGC-GGATATCT_S162_L001 12
#> SAMPLED_5348-MS-1_297-GTCTGCTA-ACGTCTCG_S297_L001 6
#> SAMPLED_5348-MS-1_381-TGCTCGTA-GTCAGATA_S381_L001 0
#> TACGTAGGGTGCAAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCACGTCGTCTGTGAAATTCCACAGCTTAACTGTGGGCGTGCAGGCGATACGGGCTGACTTGAGTACTGTAGGGGTAACTGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTTACTGGGCAGTTACTGACGCTGAGGAGCGAAAGCATGGGTAGCAAACAGG
#> SAMPLED_5080-MS-1_307-ATAGTACC-ACGTCTCG_S307_L001 0
#> SAMPLED_5080-MS-1_313-GACATAGT-TCGACGAG_S313_L001 0
#> SAMPLED_5080-MS-1_328-GATCTACG-TCGACGAG_S328_L001 0
#> SAMPLED_5080-MS-1_339-ACTCACTG-GATCGTGT_S339_L001 13
#> SAMPLED_5348-MS-1_162-ACGTGCGC-GGATATCT_S162_L001 0
#> SAMPLED_5348-MS-1_297-GTCTGCTA-ACGTCTCG_S297_L001 0
#> SAMPLED_5348-MS-1_381-TGCTCGTA-GTCAGATA_S381_L001 0
#> TACGTAGGTGACAAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAGCGCAGGCGGTCTGTTTAGTCTAATGTGAAAGCCCACGGCTTAACCGTGGAACGGCATTGGAAACTGACAGACTTGAATGTAGAAGAGGAAAATGGAATTCCAAGTGTAGCGGTGGAATGCGTAGATATTTGGAGGAACACCAGTGGCGAAGGCGATTTTCTGGTCTAACATTGACGCTGAGGCTCGAAAGCGTGGGGAGCGAACAGG
#> SAMPLED_5080-MS-1_307-ATAGTACC-ACGTCTCG_S307_L001 0
#> SAMPLED_5080-MS-1_313-GACATAGT-TCGACGAG_S313_L001 0
#> SAMPLED_5080-MS-1_328-GATCTACG-TCGACGAG_S328_L001 0
#> SAMPLED_5080-MS-1_339-ACTCACTG-GATCGTGT_S339_L001 0
#> SAMPLED_5348-MS-1_162-ACGTGCGC-GGATATCT_S162_L001 13
#> SAMPLED_5348-MS-1_297-GTCTGCTA-ACGTCTCG_S297_L001 0
#> SAMPLED_5348-MS-1_381-TGCTCGTA-GTCAGATA_S381_L001 0
#> TACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTAGATAAGTCTGAAGTTAAAGGCTGTGGCTTAACCATAGTACGCTTTGGAAACTGTTTAACTTGAGTGCAAGAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGCTTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG
#> SAMPLED_5080-MS-1_307-ATAGTACC-ACGTCTCG_S307_L001 0
#> SAMPLED_5080-MS-1_313-GACATAGT-TCGACGAG_S313_L001 0
#> SAMPLED_5080-MS-1_328-GATCTACG-TCGACGAG_S328_L001 0
#> SAMPLED_5080-MS-1_339-ACTCACTG-GATCGTGT_S339_L001 0
#> SAMPLED_5348-MS-1_162-ACGTGCGC-GGATATCT_S162_L001 3
#> SAMPLED_5348-MS-1_297-GTCTGCTA-ACGTCTCG_S297_L001 0
#> SAMPLED_5348-MS-1_381-TGCTCGTA-GTCAGATA_S381_L001 0