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39 results for “Shotgun metagenomics”
Supplementary material 7 from: Garrido-Sanz L, Senar MÀ, Piñol J (2020) Estimation of the relative abundance of species in artificial mixtures of insects using low-coverage shotgun metagenomics. Metabarcoding and Metagenomics 4: e48281. https://doi.org/10.3897/mbmg.4.48281
: Data type: Excel table
Supplementary material 2 from: Garrido-Sanz L, Senar MÀ, Piñol J (2020) Estimation of the relative abundance of species in artificial mixtures of insects using low-coverage shotgun metagenomics. Metabarcoding and Metagenomics 4: e48281. https://doi.org/10.3897/mbmg.4.48281
: Data type: Excel table
Supplementary material 1 from: Garrido-Sanz L, Senar MÀ, Piñol J (2020) Estimation of the relative abundance of species in artificial mixtures of insects using low-coverage shotgun metagenomics. Metabarcoding and Metagenomics 4: e48281. https://doi.org/10.3897/mbmg.4.48281
: Data type: Boxplot
Benchmark data for shotgun metagenomics
Open the record for dataset details and reuse information.
Supplementary material 1 from: Magesh S, Jonsson V, Bengtsson-Palme J (2019) Mumame: a software tool for quantifying gene-specific point-mutations in shotgun metagenomic data. Metabarcoding and Metagenomics 3: e36236. https://doi.org/10.3897/mbmg.3.36236
Table S1
Supplementary material 2 from: Magesh S, Jonsson V, Bengtsson-Palme J (2019) Mumame: a software tool for quantifying gene-specific point-mutations in shotgun metagenomic data. Metabarcoding and Metagenomics 3: e36236. https://doi.org/10.3897/mbmg.3.36236
Figure S1
Supplementary material 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
Table S5. Data set of the ITS2 barcode.: Explanation note: Data set of the ITS2 barcode.
Supplementary material 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
Table S4. Data set of the ITS1 barcode.: Explanation note: Data set of the ITS1 barcode.
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.
Simulted simplied metagenomics shotgun
<p>Simplified metagenomics simulation, aiming at producing a small dataset that will produce contigs when assembled and with human reads to test decontamination. Each read name contains the reference it's taken from.</p>
Assessing the Performance of Shotgun Metagenomics in the Diagnosis of Complex Prosthetic Joint Infections
ClinicalTrials.gov study NCT06062251. IPD Sharing: YES. Countries: 1. Publications: 0.
Triglyceride Reduction in Mice Receiving Gut Microbiota Transplants from Patients with Chronic Hepatitis B: A Whole Metagenomic Shotgun Sequencing Study
Open the record for dataset details and reuse information.
Shotgun metagenomic profiling of human fecal microbiota before and after aerobic exercise intervention
GEO Series GSE314617. feces metagenome. 66 samples. Type: Other.
ScienceDex guides
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