Get a data.frame containing the given report in a strollur object
Arguments
- data,
a strollur object
- type,
string containing the type of report you would like. Options include: "fasta", "sequences", "sequence_bin_assignments", "sequence_taxonomy", "bin_taxonomy", "bin_representatives", "sample_assignments", "metadata", "references", "sequence_scrap", "bin_scrap". If you have added custom reports for alignment, contigs_assembly or chimeras, you can get those as well. Default = "sequences".
- bin_type,
string containing the bin type you would like a bin_taxonomy report for. Default = "otu".
Examples
# First let's create a dataset from the \href{https://mothur.org/wiki/miseq_sop/}{MiSeq_SOP}
miseq <- miseq_sop_example()
#> Added 2425 sequences.
#> Assigned 2425 sequence abundances.
#> Assigned 2425 sequence taxonomies.
#> Assigned 531 otu bins.
#> Assigned 2425 asv bins.
#> Assigned 63 phylotype bins.
#> Assigned 19 samples to treatments.
#> Assigned 531 otu bin taxonomies.
#> Assigned 531 otu bin representative sequences.
#> Added metadata.
#> Added 2 resource references.
#> Added a contigs_report.
# To get the FASTA data
fasta <- xdev_report(data = miseq, type = "fasta")
head(fasta, n = 10)
#> sequence_names
#> 1 M00967_43_000000000-A3JHG_1_2101_16474_12783
#> 2 M00967_43_000000000-A3JHG_1_1113_12711_3318
#> 3 M00967_43_000000000-A3JHG_1_2108_14707_9807
#> 4 M00967_43_000000000-A3JHG_1_1110_4126_16552
#> 5 M00967_43_000000000-A3JHG_1_2102_8408_13436
#> 6 M00967_43_000000000-A3JHG_1_1107_22580_21773
#> 7 M00967_43_000000000-A3JHG_1_1108_14299_17220
#> 8 M00967_43_000000000-A3JHG_1_1114_8059_18290
#> 9 M00967_43_000000000-A3JHG_1_2112_9811_9982
#> 10 M00967_43_000000000-A3JHG_1_2103_25452_6018
#> sequences
#> 1 TAC--GG-AG-GAT--GCG-A-G-C-G-T-T--AT-C-CGTGAT--TT-A-T-T--GG-GT--TT-A-AA-GG-GT-GC-G-TA-GGC-G-G-A-CA-G-T-T-AA-G-T-C-A-G-C-G-G--TA-A-AA-TT-G-A-GA-GG--CT-C-AA-C-C-T-C-T-T-C--CC-G-C-CGTT-GAAAC-TG-A-TTGTC-TTGA-GT-GG-GC-GA-G-A---AG-T-A-TGTGGAATGCGTGGTGT-AGCGGT-GAAATGCATAG-AT-A-TC-AC-GC-AG-AACTCCGAT-TGCGAAGGCA------GCATA-CCG-G-CG-CC-C-A-ACTGACG-CTGA-AGCA-CGAAA-GCG-TGGGT-ATC-GAACAGG
#> 2 TAC--GT-AG-GGG--GCA-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-C-T--GG-GT--GT-A-AA-GG-GA-GC-G-TA-GGC-G-G-C-CA-T-G-C-AA-G-T-C-A-G-A-A-G--TG-A-AA-AC-C-C-GG-GG--CT-C-AA-C---C-C-TGG-G-AGT-G-C-TTTT-GAAAC-TG-T-GCGGC-TAGA-GT-GT-CG-GA-G-G---GG-T-A-AGTGGAATTCCTAGTGT-AGCGGT-GAAATGCGTAG-AT-A-TT-AG-GA-GG-AACACCAGT-GGCGAAGGCG------GCTTA-CTG-G-AC-GA-T-G-ACTGACG-CTGA-GGCT-CGAAA-GCG-TGGGT-ATC-GAACAGG
#> 3 TAC--GG-AG-GAT--GCG-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-C-T--GG-GT--GT-A-AA-GG-GA-GC-G-TA-GAC-G-G-C-GG-C-G-C-AA-G-T-C-T-G-A-A-G--TG-A-AA-GC-C-C-GT-GG--CT-C-AA-C-C-G-C-G-G-A-ACC-G-C-TTTG-GAAAC-TG-C-GAGGC-TGGA-GT-GC-TG-GA-G-A---GG-T-A-AGCGGAATTCCTGGTGT-AGCGGT-GAAATGCGTAG-AT-A-TC-AG-GA-GG-AACACCGGT-GGCGAAGGCG------GCTTA-CTG-G-AC-AG-T-G-ACTGACG-TTGA-GGCT-CGAAA-GCG-TGGGG-AGC-GAACAGG
#> 4 TAC--GG-AG-GAT--TCA-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-T-T--GG-GT--TT-A-AA-GG-GT-GC-G-TA-GGC-G-G-G-CT-G-T-T-AA-G-T-C-A-G-C-G-G--TC-A-AA-TG-T-C-GG-GG--CT-C-AA-C-C-C-C-G-G-C--CT-G-C-CGTT-GAAAC-TG-G-CGGCC-TCGA-GT-GG-GC-GA-G-A---AG-T-A-TGCGGAATGCGTGGTGT-AGCGGT-GAAATGCATAG-AT-A-TC-AC-GC-AG-AACTCCGAT-TGCGAAGGCA------GCATA-CCG-G-CG-CC-C-T-ACTGACG-CTGA-GGCA-CGAAA-GCG-TGGGT-ATC-GAACAGG
#> 5 TAC--GG-AG-GGG--GCA-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-C-T--GG-GT--GT-A-AA-GG-GA-GC-G-TA-GGC-G-G-C-AG-T-G-C-AA-G-T-C-A-G-A-A-G--TG-A-AA-GC-C-C-AA-GG--CT-C-AA-C---C-A-TGG-G-ACT-G-C-TTTT-GAAAC-TG-T-ACAGC-TAGA-TT-GC-AG-GA-G-A---GG-T-A-AGTGGAATTCCTAGTGT-AGCGGT-GAAATGCGTAG-AT-A-TT-AG-GA-GG-AACACCAGT-GGCGAAGGCG------GCTTA-CTG-G-AC-TG-T-A-AATGACG-CTGA-GGCT-CGAAA-GCG-TGGGG-AGC-AAACAGG
#> 6 TAC--GG-AG-GAT--GCG-A-G-C-G-T-T--AT-C-CCG-AT--TT-A-T-T--GG-GT--TT-A-AA-GG-GT-GC-G-TA-GGC-G-G-G-AT-G-C-C-AA-G-T-C-A-G-C-G-G--TA-A-AA-AT-G-C-GG-TG--CT-C-AA-C-G-C-C-G-T-C--GA-G-C-CGTT-GAAAC-TG-G-CGTTC-TTGA-GT-GG-GC-GA-G-A---AG-T-A-TGCGGAATGCGTGGTGT-AGCGGT-GAAATGCATAG-AT-A-TC-AC-AC-AG-AACTCCGAT-TGCGAAGGCA------GCATA-CCG-G-CG-CC-C-T-ACTGACG-CTGA-GGCA-CGAAA-GCG-TGGGT-ATC-GAACAGG
#> 7 TAC--GT-AG-GGG--GCA-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-C-T--GG-GT--GT-A-AA-GG-GA-GC-G-TA-GAC-G-G-C-TG-T-G-C-AA-G-T-C-T-G-A-A-G--TG-A-AA-TG-C-C-GG-GG--CT-C-AA-C-C-C-C-G-G-A-ACT-G-C-TTTG-GAAAC-TG-T-ACAGC-TAGA-GT-GC-AG-GA-G-G---GG-T-G-AGCGGAATTCCTAGTGT-AGCGGT-GAAATGCGTAG-AT-A-TT-AG-GA-GG-AACACCGGT-GGCGAAGGCG------GCTCA-CTG-G-AC-TG-T-A-ACTGACG-TTGA-GGCT-CGAAA-GCG-TGGGG-AGC-AAACAGG
#> 8 GAC--GGAGG-GAT--GCG-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-T-T--GG-GT--TT-A-AA-GG-GT-GC-G-TA-GGC-G-G-A-TC-G-T-T-AA-G-T-C-A-G-T-G-G--TC-A-AA-TT-G-A-GG-GG--CT-C-AA-C-C-C-C-T-T-C--CC-G-C-CATT-GAAAC-TG-G-CGATC-TTGA-GT-GG-AA-GA-G-A---AG-T-A-TGCGGAATGCGTGGTGT-AGCGGT-GAAATGCATAG-AT-A-TC-AC-GC-AG-AACCCCGAT-TGCGAAGGCA------GCATG-CCG-G-CT-TC-C-T-ACTGACG-CTGA-AGCA-CGAAA-GCG-TGGGG-ATC-GAACAGG
#> 9 TAC--GT-AG-GGG--GCA-A-G-C-G-T-T--GT-C-CGG-AT--TT-A-C-T--GG-GT--GT-A-AA-GG-GC-GT-G-CA-GCC-G-G-G-AA-G-A-C-AA-G-T-C-A-G-A-T-G--TG-A-AA-TC-C-C-GC-GG--CT-C-AA-C-C-G-C-G-G-A-ACT-G-C-ATTC-GAAAC-TG-T-TTTTC-TTGA-GT-AC-CG-GA-G-A---GG-T-C-ATCGGAATTCCTTGTGT-AGCGGT-GAAATGCGTAG-AT-A-TA-AT-GA-AG-AACACCAGT-GGCGAAGGCG------GATGA-CTG-G-AC-GG-C-A-ACTGACG-GTGA-GGCG-CGAAA-GCG-TGGGG-AGC-AAACAGG
#> 10 TAC--GG-AG-GAT--GCG-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-T-T--GG-GT--TT-A-AA-GG-GTGGC-G-CA-GGC-G-G-G-AT-G-C-C--A-G-T-C-A-G-C-G-G--TC-A-AA-TT-T-C-GG-GG--CT-C-AA-C-C-C-C-G-A-C--CT-G-C-CGTT-GAAAC-TG-G-TGTCC-TAGA-GT-GG-GC-GA-G-A---AG-T-A-TGCGGAATGCGTGGTGT-AGCGGT-GAAATGCATAG-AT-A-TC-AC-GC-AG-AACTCCGAT-TGCGAAGGCA------GCATA-CCG-G-CG-CC-C-G-ACTGACG-CTCA-TGCA-CGAAA-GCG-TGGGT-ATC-GAACAGG
# To get a report about the FASTA data
sequence_report <- xdev_report(data = miseq, type = "sequences")
head(sequence_report, n = 10)
#> id start end length ambig
#> 1 M00967_43_000000000-A3JHG_1_2101_16474_12783 1 375 253 0
#> 2 M00967_43_000000000-A3JHG_1_1113_12711_3318 1 375 253 0
#> 3 M00967_43_000000000-A3JHG_1_2108_14707_9807 1 375 253 0
#> 4 M00967_43_000000000-A3JHG_1_1110_4126_16552 1 375 252 0
#> 5 M00967_43_000000000-A3JHG_1_2102_8408_13436 1 375 253 0
#> 6 M00967_43_000000000-A3JHG_1_1107_22580_21773 1 375 252 0
#> 7 M00967_43_000000000-A3JHG_1_1108_14299_17220 1 375 253 0
#> 8 M00967_43_000000000-A3JHG_1_1114_8059_18290 1 375 253 0
#> 9 M00967_43_000000000-A3JHG_1_2112_9811_9982 1 375 253 0
#> 10 M00967_43_000000000-A3JHG_1_2103_25452_6018 1 375 252 0
#> longest_homopolymer num_n
#> 1 4 0
#> 2 5 0
#> 3 4 0
#> 4 4 0
#> 5 5 0
#> 6 5 0
#> 7 5 0
#> 8 4 0
#> 9 5 0
#> 10 4 0
# To get the sequence bin assignments
bin_assignments <- xdev_report(data = miseq, type = "sequence_bin_assignments",
bin_type = "otu")
head(bin_assignments, n = 10)
#> otu_id seq_id
#> 1 Otu001 M00967_43_000000000-A3JHG_1_1111_20933_6700
#> 2 Otu001 M00967_43_000000000-A3JHG_1_1113_17095_9759
#> 3 Otu001 M00967_43_000000000-A3JHG_1_1114_22144_24942
#> 4 Otu001 M00967_43_000000000-A3JHG_1_1112_5981_8948
#> 5 Otu001 M00967_43_000000000-A3JHG_1_2106_5509_18056
#> 6 Otu001 M00967_43_000000000-A3JHG_1_1112_18411_17052
#> 7 Otu001 M00967_43_000000000-A3JHG_1_1101_20262_22075
#> 8 Otu001 M00967_43_000000000-A3JHG_1_1114_13556_18457
#> 9 Otu001 M00967_43_000000000-A3JHG_1_2114_12634_10967
#> 10 Otu001 M00967_43_000000000-A3JHG_1_1102_18640_14309
# To get the sample treatment assignments
xdev_report(data = miseq, type = "sample_assignments")
#> samples treatments
#> 1 F3D0 Early
#> 2 F3D1 Early
#> 3 F3D141 Late
#> 4 F3D142 Late
#> 5 F3D143 Late
#> 6 F3D144 Late
#> 7 F3D145 Late
#> 8 F3D146 Late
#> 9 F3D147 Late
#> 10 F3D148 Late
#> 11 F3D149 Late
#> 12 F3D150 Late
#> 13 F3D2 Early
#> 14 F3D3 Early
#> 15 F3D5 Early
#> 16 F3D6 Early
#> 17 F3D7 Early
#> 18 F3D8 Early
#> 19 F3D9 Early
# To get a report about sequence classifications
sequence_taxonomy_report <- xdev_report(data = miseq,
type = "sequence_taxonomy")
head(sequence_taxonomy_report, n = 10)
#> sequence_names levels
#> 1 M00967_43_000000000-A3JHG_1_2101_16474_12783 1
#> 2 M00967_43_000000000-A3JHG_1_2101_16474_12783 2
#> 3 M00967_43_000000000-A3JHG_1_2101_16474_12783 3
#> 4 M00967_43_000000000-A3JHG_1_2101_16474_12783 4
#> 5 M00967_43_000000000-A3JHG_1_2101_16474_12783 5
#> 6 M00967_43_000000000-A3JHG_1_2101_16474_12783 6
#> 7 M00967_43_000000000-A3JHG_1_1113_12711_3318 1
#> 8 M00967_43_000000000-A3JHG_1_1113_12711_3318 2
#> 9 M00967_43_000000000-A3JHG_1_1113_12711_3318 3
#> 10 M00967_43_000000000-A3JHG_1_1113_12711_3318 4
#> taxonomies confidences
#> 1 Bacteria 100
#> 2 "Bacteroidetes" 100
#> 3 "Bacteroidia" 99
#> 4 "Bacteroidales" 99
#> 5 "Porphyromonadaceae" 88
#> 6 "Porphyromonadaceae"_unclassified 88
#> 7 Bacteria 100
#> 8 Firmicutes 100
#> 9 Clostridia 100
#> 10 Clostridiales 100
# To get a report about bin classifications for 'otu' data
otu_taxonomy_report <- xdev_report(data = miseq,
type = "bin_taxonomy",
bin_type = "otu")
head(otu_taxonomy_report, n = 10)
#> bin_names levels taxonomies confidences
#> 1 Otu001 1 Bacteria 100
#> 2 Otu001 2 "Bacteroidetes" 100
#> 3 Otu001 3 "Bacteroidia" 100
#> 4 Otu001 4 "Bacteroidales" 100
#> 5 Otu001 5 "Porphyromonadaceae" 100
#> 6 Otu001 6 "Porphyromonadaceae"_unclassified 100
#> 7 Otu002 1 Bacteria 100
#> 8 Otu002 2 "Bacteroidetes" 100
#> 9 Otu002 3 "Bacteroidia" 100
#> 10 Otu002 4 "Bacteroidales" 100
# To get a report about bin classifications for 'asv' data
asv_taxonomy_report <- xdev_report(data = miseq, type = "bin_taxonomy",
bin_type = "asv")
head(asv_taxonomy_report, n = 10)
#> bin_names levels taxonomies confidences
#> 1 Asv0001 1 Bacteria 100
#> 2 Asv0001 2 "Bacteroidetes" 100
#> 3 Asv0001 3 "Bacteroidia" 100
#> 4 Asv0001 4 "Bacteroidales" 100
#> 5 Asv0001 5 "Porphyromonadaceae" 100
#> 6 Asv0001 6 "Porphyromonadaceae"_unclassified 100
#> 7 Asv0002 1 Bacteria 100
#> 8 Asv0002 2 "Bacteroidetes" 100
#> 9 Asv0002 3 "Bacteroidia" 100
#> 10 Asv0002 4 "Bacteroidales" 100
# To get a report about bin classifications for 'phylotype' data
phylotype_taxonomy_report <- xdev_report(data = miseq, type = "bin_taxonomy",
bin_type = "phylotype")
head(phylotype_taxonomy_report, n = 10)
#> bin_names levels taxonomies confidences
#> 1 Phylo01 1 Bacteria 100
#> 2 Phylo01 2 Firmicutes 100
#> 3 Phylo01 3 Clostridia 100
#> 4 Phylo01 4 Clostridiales 100
#> 5 Phylo01 5 Lachnospiraceae 100
#> 6 Phylo01 6 Lachnospiraceae_unclassified 100
#> 7 Phylo02 1 Bacteria 100
#> 8 Phylo02 2 "Bacteroidetes" 100
#> 9 Phylo02 3 "Bacteroidia" 100
#> 10 Phylo02 4 "Bacteroidales" 100
# To get the 'otu' bin representative sequences
otu_bin_reps <- xdev_report(data = miseq, type = "bin_representatives",
bin_type = "otu")
head(otu_bin_reps, n = 10)
#> otu_names representative_names
#> 1 Otu001 M00967_43_000000000-A3JHG_1_1108_14299_17220
#> 2 Otu002 M00967_43_000000000-A3JHG_1_1106_22705_6123
#> 3 Otu003 M00967_43_000000000-A3JHG_1_1101_15533_5293
#> 4 Otu004 M00967_43_000000000-A3JHG_1_1105_25642_17588
#> 5 Otu005 M00967_43_000000000-A3JHG_1_2102_7041_13746
#> 6 Otu006 M00967_43_000000000-A3JHG_1_1106_17565_8490
#> 7 Otu007 M00967_43_000000000-A3JHG_1_1109_13330_21597
#> 8 Otu008 M00967_43_000000000-A3JHG_1_1110_5315_13833
#> 9 Otu009 M00967_43_000000000-A3JHG_1_2109_27297_13184
#> 10 Otu010 M00967_43_000000000-A3JHG_1_1101_9620_19745
#> representative_sequences
#> 1 TAC--GT-AG-GGG--GCA-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-C-T--GG-GT--GT-A-AA-GG-GA-GC-G-TA-GAC-G-G-C-TG-T-G-C-AA-G-T-C-T-G-A-A-G--TG-A-AA-TG-C-C-GG-GG--CT-C-AA-C-C-C-C-G-G-A-ACT-G-C-TTTG-GAAAC-TG-T-ACAGC-TAGA-GT-GC-AG-GA-G-G---GG-T-G-AGCGGAATTCCTAGTGT-AGCGGT-GAAATGCGTAG-AT-A-TT-AG-GA-GG-AACACCGGT-GGCGAAGGCG------GCTCA-CTG-G-AC-TG-T-A-ACTGACG-TTGA-GGCT-CGAAA-GCG-TGGGG-AGC-AAACAGG
#> 2 TAC--GT-AG-GGG--GCA-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-C-T--GG-GT--GT-A-AA-GG-GA-GC-G-CA-GAC-G-G-C-TG-T-G-C-AA-G-T-C-T-G-G-A-G--TG-A-AA-GG-C-G-GG-GG--CC-C-AA-C-C-C-C-C-G-G-ACT-G-C-TCTG-GAAAC-TG-T-AAAGC-TGGA-GT-GC-AG-GA-G-A---GG-T-A-AGCGGAATTCCTAGTGT-AGCGGT-GAAATGCGTAG-AT-A-TT-AG-GA-GG-AACACCAGT-GGCGAAGGCG------GCTTA-CTG-G-AC-TG-C-A-ACTGACG-TTGA-GGCT-CGAAA-GCG-TGGGT-ATC-GAACAGG
#> 3 TAC--GG-AG-GAT--GCG-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-C-T--GG-GT--GT-A-AA-GG-GA-GC-G-TA-GAC-G-G-C-GA-T-G-C-AA-G-T-C-T-G-A-A-G--TG-A-AA-GG-C-G-GG-GG--CC-C-AA-C-C-C-C-C-G-G-ACT-G-C-TTTG-GAAAC-TG-T-ATAGC-TGGA-GT-GC-AG-GA-G-A---GG-T-A-AGTGGAATTCCTAGTGT-AGCGGT-GAAATGCGTAG-AT-A-TT-AG-GA-GG-AACACCAGT-GGCGAAGGCG------GCTTA-CTG-G-AC-TG-T-A-ACTGACG-TTGA-GGCT-CGAAA-GCG-TGGGG-AGC-AAACAGG
#> 4 TAC--GT-AG-GTG--GCA-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-C-T--GG-GT--GT-A-AA-GG-GC-GT-G-TA-GGC-G-G-G-AC-T-G-C-AA-G-T-C-A-G-A-T-G--TG-A-AA-CC-C-A-TG-GG--CT-C-AA-C-C-C-A-T-G-G-CCT-G-C-ATTT-GAAAC-TG-T-AGTTC-TTGA-GT-GA-TG-GA-G-A---GG-C-A-GGCGGAATTCCGTGTGT-AGCGGT-GAAATGCGTAG-AT-A-TA-CG-GA-GG-AACACCAGT-GGCGAAGGCG------GCCTG-CTG-G-AC-AT-T-A-ACTGACG-CTGA-GGCG-CGAAA-GCG-TGGGG-AGC-AAACAGG
#> 5 TAC--GT-AG-GGG--GCG-A-G-C-G-T-T--AT-C-CGG-AT--TC-A-T-T--GG-GC--GT-A-AA-GC-GC-GC-G-CA-GGC-G-G-A-CT-C-A-T-AA-G-C-G-G-A-G-C-C--TT-T-AA-TC-T-T-GG-GG--CT-T-AA-C-C-T-C-A-A-G-T-C-G-G-GCCC-CGAAC-TG-T-GAGTC-TCGA-GT-GT-GG-TA-G-G---GG-A-A-GGCGGAATTCCCGGTGT-AGCGGT-GGAATGCGCAG-AT-A-TC-GG-GA-AG-AACACCGAT-GGCGAAGGCA------GCCTT-CTG-G-GC-CA-T-C-ACTGACG-CTGA-GGCG-CGAAA-GCT-AGGGG-AGC-AAACAGG
#> 6 TAC--GT-AT-GGA--GCA-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-C-T--GG-GT--GT-A-AA-GG-GA-GC-G-TA-GGC-G-G-C-AT-A-C-C-AA-G-C-C-T-G-A-T-G--TG-A-AA-AC-C-C-GG-GG--CC-C-AA-C-C-C-C-G-G-G-AGT-G-C-ATTG-GGAAC-TG-G-CAAGC-TAGA-GT-GT-CG-GA-G-A---GG-C-A-GGCGGAATTCCTAGTGT-AGCGGT-GAAATGCGTAG-AT-A-TT-AG-GA-GG-AACACCAGT-GGCGAAGGCG------GCCTG-CTG-G-AC-GA-T-G-ACTGACG-CTGA-GGCT-CGAAA-GCG-TGGGG-AGC-AAACAGG
#> 7 TAC--GT-AT-GGT--GCA-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-C-T--GG-GT--GT-A-AA-GG-GA-GC-G-CA-GGC-G-G-T-AC-G-G-C-AA-G-T-C-T-G-A-T-G--TG-A-AA-GC-C-C-GG-GG--CT-C-AA-C-C-C-C-G-G-T-ACT-G-C-ATTG-GAAAC-TG-C-CGGAC-TGGA-GT-GT-CG-GA-G-G---GG-T-A-AGCGGAATTCCTGGTGT-AGCGGT-GAAATGCGTAG-AT-A-TC-AG-GA-GG-AACACCGGT-GGCGAAGGCG------GCTTA-CTG-G-AC-GA-T-G-ACTGACG-CTGA-GGCT-CGAAA-GCG-TGGGG-AGC-AAACAGG
#> 8 TAC--GT-AG-GGG--GCA-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-C-T--GG-GT--GT-A-AA-GG-GG-GC-G-CA-GAC-G-G-C-AG-C-G-C-AA-G-C-C-A-G-G-A-G--TG-A-AA-GC-C-C-GG-GG--CC-C-AA-C-C-C-C-G-G-G-ACT-G-C-TCTT-GGAAC-TG-C-GCGGC-TGGA-GT-GC-AG-GA-G-G---GG-C-A-GGCGGAATTCCTGGTGT-AGCGGT-GAAATGCGTAG-AT-A-TC-AG-GA-GG-AACACCGGT-GGCGAAGGCG------GCCTG-CTG-G-AC-TG-C-G-ACTGACG-TTGA-GGCC-CGAAA-GCG-TGGGG-AGC-AAACAGG
#> 9 TAC--GG-AG-GAT--GCG-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-T-T--GG-GT--TT-A-AA-GG-GT-GC-G-TA-GGC-G-G-G-AT-G-C-C-AA-G-T-C-A-G-C-G-G--TA-A-AA-AT-G-C-GG-TG--CT-C-AA-C-G-C-C-G-T-C--GA-G-C-CGTT-GAAAC-TG-G-CGTTC-TTGA-GT-GG-GC-GA-G-A---AG-T-A-TGCGGAATGCGTGGTGT-AGCGGT-GAAATGCATAG-AT-A-TC-AC-GC-AG-AACTCCGAT-TGCGAAGGCA------GCATA-CCG-G-CG-CT-C-A-ACTGACG-CTCA-TGCA-CGAAA-GTG-CGGGG-ATC-AAACAGG
#> 10 TAC--GG-AG-GAT--CCG-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-C-T--GG-GT--GT-A-AA-GG-GT-GC-G-TA-GGC-G-G-C-CT-T-G-C-AA-G-T-C-A-G-A-A-G--TG-A-AA-TC-C-A-TG-GG--CT-T-AA-C-C-C-G-T-G-A-ACT-G-C-TTTT-GAAAC-TG-T-AGGGC-TTGA-GT-GA-AG-TA-G-A---GG-C-A-GGCGGAATTCCCGGTGT-AGCGGT-GAAATGCGTAG-AG-A-TC-GG-GA-GG-AACACCAGT-GGCGAAGGCG------GCCTG-CTG-G-GC-TT-T-A-ACTGACG-CTGA-AGCA-CGAAA-GCG-TGGGT-AGC-AAACAGG
# To get a report about the sequences removed during your analysis:
scrapped_sequence_report <- xdev_report(data = miseq, type = "sequence_scrap")
# To get a report about the "otu" bins removed during your analysis:
scrapped_otu_report <- xdev_report(data = miseq, type = "bin_scrap",
bin_type = "otu")
# To get a report about the "phylotype" bins removed during your analysis:
scrapped_phylotype_report <- xdev_report(data = miseq, type = "bin_scrap",
bin_type = "phylotype")
# To get the metadata associated with your data:
metadata <- xdev_report(data = miseq, type = "metadata")
# To get the resource references associated with your data:
references <- xdev_report(data = miseq, type = "references")
# To get our custom report containing the contigs assembly data:
contigs_report <- xdev_report(data = miseq, type = "contigs_report")
head(contigs_report, n = 10)
#> Name Length Overlap_Length
#> 1 M00967_43_000000000-A3JHG_1_2101_16474_12783 253 250
#> 2 M00967_43_000000000-A3JHG_1_1113_12711_3318 253 249
#> 3 M00967_43_000000000-A3JHG_1_2108_14707_9807 253 249
#> 4 M00967_43_000000000-A3JHG_1_1110_4126_16552 252 249
#> 5 M00967_43_000000000-A3JHG_1_2102_8408_13436 253 249
#> 6 M00967_43_000000000-A3JHG_1_1107_22580_21773 252 250
#> 7 M00967_43_000000000-A3JHG_1_1108_14299_17220 253 249
#> 8 M00967_43_000000000-A3JHG_1_1114_8059_18290 253 249
#> 9 M00967_43_000000000-A3JHG_1_2112_9811_9982 253 249
#> 10 M00967_43_000000000-A3JHG_1_2103_25452_6018 252 249
#> Overlap_Start Overlap_End MisMatches Num_Ns Expected_Errors
#> 1 2 252 19 0 0.29461400
#> 2 2 251 0 0 0.00183396
#> 3 2 251 0 0 0.00196774
#> 4 2 251 4 0 0.05629750
#> 5 2 251 0 0 0.00259554
#> 6 1 251 8 0 0.05068300
#> 7 2 251 0 0 0.00215398
#> 8 3 252 11 0 0.05362360
#> 9 2 251 0 0 0.00184906
#> 10 2 251 18 0 0.54816100