aspergillus candidus link : fries  (ATCC)

Journal: Briefings in Bioinformatics

Article Title: Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data

doi: 10.1093/bib/bbae642

Figure Lengend Snippet: Summary of the ONT 16S rRNA gene data used in this study.

Article Snippet: The number of non-chimeric consensus sequences produced by CONCOMPRA was close to the number of bacteria present in the mock (19.5 ± 2.4 sd) and the average sequence similarity between the consensus sequences and the best-matching genome-derived 16S rRNA gene sequences ( https://www.atcc.org/products/msa-1002 ) was ≥99.9% for the four samples ( ).

Techniques: Sequencing

Journal: Briefings in Bioinformatics

Article Title: Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data

doi: 10.1093/bib/bbae642

Figure Lengend Snippet: Similarity of the sequencing data and the consensus sequences to the reference 16S mock community. The blast-based percentage similarity to the references is shown for the reads themselves (violin plots) and generated consensus sequences (box plots). The similarity to the references is shown for each 16S mock sample in a different panel: A = 16S_R9_1; B = 16S_R9_2; C = 16S_R10_43; D = 16S_R10_60. The reads (dark grey; left side of each panel) from the R10 sets (bottom row, C & D) were markedly more similar to the reference sequences (>20% of the reads were at least 98% similar to the references) than the reads from the R9 sets (>5% of the reads were at least 98% similar to the references; top row, A & B). The alternative consensus building tools (red) generated more consensus sequences, but these were less similar than the non-chimeric consensus sequences generated by CONCOMPRA (green). The chimeric consensus sequences from CONCOMPRA were the least similar (97% on average) to the reference sequences.

Article Snippet: The number of non-chimeric consensus sequences produced by CONCOMPRA was close to the number of bacteria present in the mock (19.5 ± 2.4 sd) and the average sequence similarity between the consensus sequences and the best-matching genome-derived 16S rRNA gene sequences ( https://www.atcc.org/products/msa-1002 ) was ≥99.9% for the four samples ( ).

Techniques: Sequencing, Generated

Journal: Briefings in Bioinformatics

Article Title: Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data

doi: 10.1093/bib/bbae642

Figure Lengend Snippet: Detection of the 20 different species in the bacterial mock community. The highest similarity to any of the 16S rRNA gene copy sequences to each species (colors) is shown for the different consensus building tools (rows) for the different 16S mock datasets. Only non-chimeric sequences are considered for CONCOMPRA. Species for which no consensus sequences with an identity above 99% was present are shown as hollow circles to the left of the axis. The similarity to the references is shown for each 16S mock sample in a different panel: A = 16S_R9_1; B = 16S_R9_2; C = 16S_R10_43; D = 16S_R10_60.

Article Snippet: The number of non-chimeric consensus sequences produced by CONCOMPRA was close to the number of bacteria present in the mock (19.5 ± 2.4 sd) and the average sequence similarity between the consensus sequences and the best-matching genome-derived 16S rRNA gene sequences ( https://www.atcc.org/products/msa-1002 ) was ≥99.9% for the four samples ( ).

Techniques:

Journal: Briefings in Bioinformatics

Article Title: Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data

doi: 10.1093/bib/bbae642

Figure Lengend Snippet: Sensitivity of the different consensus sequence building approaches. The highest similarity to any of the 16S rRNA gene copy sequences to each species (colors) is shown for the different consensus building tools (rows) for the gut microbiome standard. The theoretical abundance of each species (in %) in the community is shown in brackets, next to the species’ name and as the size of the circles. Only non-chimeric sequences are considered for CONCOMPRA. Species for which no consensus sequences with an identity above 99% was present are shown as hollow circles to the left of the axis.

Article Snippet: The number of non-chimeric consensus sequences produced by CONCOMPRA was close to the number of bacteria present in the mock (19.5 ± 2.4 sd) and the average sequence similarity between the consensus sequences and the best-matching genome-derived 16S rRNA gene sequences ( https://www.atcc.org/products/msa-1002 ) was ≥99.9% for the four samples ( ).

Techniques: Sequencing

Journal: Briefings in Bioinformatics

Article Title: Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data

doi: 10.1093/bib/bbae642

Figure Lengend Snippet: The relative abundance of the NS11–12 marine group in the natural 16S samples. The different clades within the NS11–12 marine group are indicated in the bar plots and cladogram by grey and black. There is no fill (white) if no distinction can be made. The community and data type are indicated in the bar plot by the color and shape of the symbol. The sequences from the DADA2 and CONCOMPRA dataset are indicated in the phylogenetic tree with a ‘D’ and a ‘C’ in the tip labels, respectively.

Article Snippet: The number of non-chimeric consensus sequences produced by CONCOMPRA was close to the number of bacteria present in the mock (19.5 ± 2.4 sd) and the average sequence similarity between the consensus sequences and the best-matching genome-derived 16S rRNA gene sequences ( https://www.atcc.org/products/msa-1002 ) was ≥99.9% for the four samples ( ).

Techniques:

Journal: Briefings in Bioinformatics

Article Title: Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data

doi: 10.1093/bib/bbae642

Figure Lengend Snippet: Summary of the ONT 16S rRNA gene data used in this study.

Article Snippet: The number of non-chimeric consensus sequences produced by CONCOMPRA was close to the number of bacteria present in the mock (19.5 ± 2.4 sd) and the average sequence similarity between the consensus sequences and the best-matching genome-derived 16S rRNA gene sequences ( https://www.atcc.org/products/msa-1002 ) was ≥99.9% for the four samples ( ).

Techniques: Sequencing

Journal: Briefings in Bioinformatics

Article Title: Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data

doi: 10.1093/bib/bbae642

Figure Lengend Snippet: Similarity of the sequencing data and the consensus sequences to the reference 16S mock community. The blast-based percentage similarity to the references is shown for the reads themselves (violin plots) and generated consensus sequences (box plots). The similarity to the references is shown for each 16S mock sample in a different panel: A = 16S_R9_1; B = 16S_R9_2; C = 16S_R10_43; D = 16S_R10_60. The reads (dark grey; left side of each panel) from the R10 sets (bottom row, C & D) were markedly more similar to the reference sequences (>20% of the reads were at least 98% similar to the references) than the reads from the R9 sets (>5% of the reads were at least 98% similar to the references; top row, A & B). The alternative consensus building tools (red) generated more consensus sequences, but these were less similar than the non-chimeric consensus sequences generated by CONCOMPRA (green). The chimeric consensus sequences from CONCOMPRA were the least similar (97% on average) to the reference sequences.

Article Snippet: The number of non-chimeric consensus sequences produced by CONCOMPRA was close to the number of bacteria present in the mock (19.5 ± 2.4 sd) and the average sequence similarity between the consensus sequences and the best-matching genome-derived 16S rRNA gene sequences ( https://www.atcc.org/products/msa-1002 ) was ≥99.9% for the four samples ( ).

Techniques: Sequencing, Generated

Journal: Briefings in Bioinformatics

Article Title: Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data

doi: 10.1093/bib/bbae642

Figure Lengend Snippet: Detection of the 20 different species in the bacterial mock community. The highest similarity to any of the 16S rRNA gene copy sequences to each species (colors) is shown for the different consensus building tools (rows) for the different 16S mock datasets. Only non-chimeric sequences are considered for CONCOMPRA. Species for which no consensus sequences with an identity above 99% was present are shown as hollow circles to the left of the axis. The similarity to the references is shown for each 16S mock sample in a different panel: A = 16S_R9_1; B = 16S_R9_2; C = 16S_R10_43; D = 16S_R10_60.

Article Snippet: The number of non-chimeric consensus sequences produced by CONCOMPRA was close to the number of bacteria present in the mock (19.5 ± 2.4 sd) and the average sequence similarity between the consensus sequences and the best-matching genome-derived 16S rRNA gene sequences ( https://www.atcc.org/products/msa-1002 ) was ≥99.9% for the four samples ( ).

Techniques:

Journal: Briefings in Bioinformatics

Article Title: Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data

doi: 10.1093/bib/bbae642

Figure Lengend Snippet: Sensitivity of the different consensus sequence building approaches. The highest similarity to any of the 16S rRNA gene copy sequences to each species (colors) is shown for the different consensus building tools (rows) for the gut microbiome standard. The theoretical abundance of each species (in %) in the community is shown in brackets, next to the species’ name and as the size of the circles. Only non-chimeric sequences are considered for CONCOMPRA. Species for which no consensus sequences with an identity above 99% was present are shown as hollow circles to the left of the axis.

Article Snippet: The number of non-chimeric consensus sequences produced by CONCOMPRA was close to the number of bacteria present in the mock (19.5 ± 2.4 sd) and the average sequence similarity between the consensus sequences and the best-matching genome-derived 16S rRNA gene sequences ( https://www.atcc.org/products/msa-1002 ) was ≥99.9% for the four samples ( ).

Techniques: Sequencing

Journal: Briefings in Bioinformatics

Article Title: Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data

doi: 10.1093/bib/bbae642

Figure Lengend Snippet: The relative abundance of the NS11–12 marine group in the natural 16S samples. The different clades within the NS11–12 marine group are indicated in the bar plots and cladogram by grey and black. There is no fill (white) if no distinction can be made. The community and data type are indicated in the bar plot by the color and shape of the symbol. The sequences from the DADA2 and CONCOMPRA dataset are indicated in the phylogenetic tree with a ‘D’ and a ‘C’ in the tip labels, respectively.

Article Snippet: The number of non-chimeric consensus sequences produced by CONCOMPRA was close to the number of bacteria present in the mock (19.5 ± 2.4 sd) and the average sequence similarity between the consensus sequences and the best-matching genome-derived 16S rRNA gene sequences ( https://www.atcc.org/products/msa-1002 ) was ≥99.9% for the four samples ( ).

Techniques: