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915 results for “metagenomics”
Supplementary material 10 from: Rajter Ľ, Dunthorn M (2021) Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data. Metabarcoding and Metagenomics 5: e69602. https://doi.org/10.3897/mbmg.5.69602
File S10
Supplementary material 6 from: Rajter Ľ, Dunthorn M (2021) Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data. Metabarcoding and Metagenomics 5: e69602. https://doi.org/10.3897/mbmg.5.69602
File S6
Supplementary material 20 from: Rajter Ľ, Dunthorn M (2021) Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data. Metabarcoding and Metagenomics 5: e69602. https://doi.org/10.3897/mbmg.5.69602
Table S1
Supplementary material 5 from: Rajter Ľ, Dunthorn M (2021) Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data. Metabarcoding and Metagenomics 5: e69602. https://doi.org/10.3897/mbmg.5.69602
File S5
Supplementary material 14 from: Rajter Ľ, Dunthorn M (2021) Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data. Metabarcoding and Metagenomics 5: e69602. https://doi.org/10.3897/mbmg.5.69602
File S14
Supplementary material 13 from: Rajter Ľ, Dunthorn M (2021) Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data. Metabarcoding and Metagenomics 5: e69602. https://doi.org/10.3897/mbmg.5.69602
File S13
Supplementary material 12 from: Rajter Ľ, Dunthorn M (2021) Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data. Metabarcoding and Metagenomics 5: e69602. https://doi.org/10.3897/mbmg.5.69602
File S12
Supplementary material 1 from: {"en": "Kolter A, Gemeinholzer B (2021) Internal transcribed spacer primer evaluation for vascular plant metabarcoding. Metabarcoding and Metagenomics 5: e68155. https://doi.org/10.3897/mbmg.5.68155"}
Supplementary files
Supplementary material 1 from: Ingala MR, Werner IE, Fitzgerald AM, Naro-Maciel E (2021) 18S rRNA amplicon sequence data (V1–V3) of the Bronx river estuary, New York. Metabarcoding and Metagenomics 5: e69691. https://doi.org/10.3897/mbmg.5.69691
Scripts used for metabarcoding analysis
Supplementary material 2 from: Ingala MR, Werner IE, Fitzgerald AM, Naro-Maciel E (2021) 18S rRNA amplicon sequence data (V1–V3) of the Bronx river estuary, New York. Metabarcoding and Metagenomics 5: e69691. https://doi.org/10.3897/mbmg.5.69691
Figure S1, Tables S1, S2
Figure 5 from: Tedersoo L, Anslan S, Bahram M, Põlme S, Riit T, Liiv I, Kõljalg U, Kisand V, Nilsson RH, Hildebrand F, Bork P, Abarenkov K (2015) Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi. MycoKeys 10: 1-43. https://doi.org/10.3897/mycokeys.10.4852
Figure 5 - Global Nonmetric Multidimensional Scaling (NMDS) graph demonstrating the relative placement of samples (lower case letters, encoded in Suppl. material 1) in the ordination space. 95% confidence ellipses are indicated for each barcode-primer pair combination. For two-dimensional solution, stress=0.191 (R2=0.875).
Figure 2 from: Tedersoo L, Anslan S, Bahram M, Põlme S, Riit T, Liiv I, Kõljalg U, Kisand V, Nilsson RH, Hildebrand F, Bork P, Abarenkov K (2015) Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi. MycoKeys 10: 1-43. https://doi.org/10.3897/mycokeys.10.4852
Figure 2 - Sample-based OTU richness as recovered by different barcode-primer pair combinations. Error bars denote standard error; different letters indicate statistically different groups.
Figure 1 from: Tedersoo L, Anslan S, Bahram M, Põlme S, Riit T, Liiv I, Kõljalg U, Kisand V, Nilsson RH, Hildebrand F, Bork P, Abarenkov K (2015) Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi. MycoKeys 10: 1-43. https://doi.org/10.3897/mycokeys.10.4852
Figure 1 - Map of ribosomal DNA indicating variable regions as well as primers used and/or discussed in this study. Primers pairs used for HTS are highlighted.
Figure 3 from: Tedersoo L, Anslan S, Bahram M, Põlme S, Riit T, Liiv I, Kõljalg U, Kisand V, Nilsson RH, Hildebrand F, Bork P, Abarenkov K (2015) Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi. MycoKeys 10: 1-43. https://doi.org/10.3897/mycokeys.10.4852
Figure 3 - Rarefied OTU accumulation curves for samples based on the (a) ITS1 and (b) ITS2 barcodes and their 95% confidence intervals.
Figure 6 from: Tedersoo L, Anslan S, Bahram M, Põlme S, Riit T, Liiv I, Kõljalg U, Kisand V, Nilsson RH, Hildebrand F, Bork P, Abarenkov K (2015) Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi. MycoKeys 10: 1-43. https://doi.org/10.3897/mycokeys.10.4852
Figure 6 - Relative abundance of fungal classes in the amplicon and metagenomics data sets divided into SSU, ITS, and LSU subsets averaged over different barcodes (amplicon data) and 14 shared samples. Asterisks in the margins indicate significant differences in recovery of classes among SSU, ITS, and LSU of metagenomics (right) and amplicon (left) data sets. Asterisks in the center indicate significant differences between the metagenomics and amplicon-bases approaches.
Figure 7 from: Tedersoo L, Anslan S, Bahram M, Põlme S, Riit T, Liiv I, Kõljalg U, Kisand V, Nilsson RH, Hildebrand F, Bork P, Abarenkov K (2015) Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi. MycoKeys 10: 1-43. https://doi.org/10.3897/mycokeys.10.4852
Figure 7 - Differences in sequence length in the ITS1 and ITS2 barcodes of 16 most abundant fungal classes as revealed based on amplicon libraries in this study. Columns, asterisks, and error bars represent mean and median values and standard deviation, respectively. Numbers inside bars indicate the number of sequences analyzed (n). Taxa are ordered by average length of the ITS1 region.
Figure 4 from: Tedersoo L, Anslan S, Bahram M, Põlme S, Riit T, Liiv I, Kõljalg U, Kisand V, Nilsson RH, Hildebrand F, Bork P, Abarenkov K (2015) Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi. MycoKeys 10: 1-43. https://doi.org/10.3897/mycokeys.10.4852
Figure 4 - Relationship between connectance and adjusted coefficient of determination (R2adj) for floristic variables across different barcode-primer pair combinations based on (a) Bray-Curtis distance and (b) Hellinger distance. Pointed line indicates correlation in the ITS1Fngs-ITS2 data set (filled circles), covering eight connectance classes (C<0.45). Open circles, other ITS1 and ITS2 primer pairs; triangles, SSU barcodes; rectangles, LSU barcodes.
Figure 2 from: Tedersoo L, Liiv I, Kivistik PA, Anslan S, Kõljalg U, Bahram M (2016) Genomics and metagenomics technologies to recover ribosomal DNA and single-copy genes from old fruit-body and ectomycorrhiza specimens. MycoKeys 13: 1-20. https://doi.org/10.3897/mycokeys.13.8140
Figure 2 - Impact of maximum obtained DNA concentration and number of Illumina HiSeq reads on the size of all scaffolds (A, B) and largest nuclear rDNA scaffold (C, D). Regular straight lines and dotted lines indicate linear and better fitting logarithmic relationships, respectively.
Figure 1 from: Tedersoo L, Liiv I, Kivistik PA, Anslan S, Kõljalg U, Bahram M (2016) Genomics and metagenomics technologies to recover ribosomal DNA and single-copy genes from old fruit-body and ectomycorrhiza specimens. MycoKeys 13: 1-20. https://doi.org/10.3897/mycokeys.13.8140
Figure 1 - Effect of specimen age on the recovery of reads in the Illumina HiSeq run. Closed circles, 'old' fruit-bodies; shaded circles, 'regular' fruit-bodies; open circles, 'unsequenced' fruit-bodies; shaded triangles, ectomycorrhizal root tips representing unique rare lineages; open triangles, 'unsequenced' ectomycorrhizal root tips.
Data for "Capturing variation in metagenomic assembly graphs with MetaCortex".
<p>Data for paper "Capturing variation in metagenomic assembly graphs with MetaCortex". Includes all assemblies, simulated reads, and simulated genomes.</p>
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