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The top row presents results for Nanopore data, and the bottom row for HiFi data. a Contamination level in contigs longer than 1 Mbp. The percentage above each plot indicates the overall proportion of long contaminated contigs (with contamination over 5%). b Number of clipping events supported by at least 10 reads. c Number of regions over 1,000 bp with no apparent read coverage. d Proportion of predicted proteins which are ≥90% the length of their best-matching known protein in a <t>reference</t> database (from contigs with more than 10x coverage). In ( a ), results are aggregated across assemblies of the three data sets: Human Gut, <t>Zymo</t> Fecal Reference and Soil, but separated by both data set and assembler in b , c , and d . The boxplot elements are the median (horizontal bar), 25th and 75th percentiles (box limits Q1 and Q3), Q1-1.5*IQR and Q3+1.5*IQR (whiskers, IQR = Q3 − Q1) and outliers. Summary statistics in ( a ) (n, min, max, median, 25th and 75th percentiles, lower whisker, upper whisker): Nanopore-nanoMDBG (1006, 0, 28.47, 0.15, 0.04, 0.46, 0, 1.09); metaMDBG (549, 0, 28.07, 0.18, 0.05, 0.6, 0, 1.37); metaFlye (326, 0, 18.56, 0.13, 0.03, 0.39, 0, 0.92): HiFi-metaMDBG (1239, 0, 28.27, 0.14, 0.04, 0.41, 0, 0.96); hifiasm-meta (667, 0, 23.3, 0.15, 0.05, 0.445, 0, 1.03); metaFlye (362, 0, 20.41, 0.14, 0.04, 0.4, 0, 0.93).
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The top row presents results for Nanopore data, and the bottom row for HiFi data. a Contamination level in contigs longer than 1 Mbp. The percentage above each plot indicates the overall proportion of long contaminated contigs (with contamination over 5%). b Number of clipping events supported by at least 10 reads. c Number of regions over 1,000 bp with no apparent read coverage. d Proportion of predicted proteins which are ≥90% the length of their best-matching known protein in a <t>reference</t> database (from contigs with more than 10x coverage). In ( a ), results are aggregated across assemblies of the three data sets: Human Gut, <t>Zymo</t> Fecal Reference and Soil, but separated by both data set and assembler in b , c , and d . The boxplot elements are the median (horizontal bar), 25th and 75th percentiles (box limits Q1 and Q3), Q1-1.5*IQR and Q3+1.5*IQR (whiskers, IQR = Q3 − Q1) and outliers. Summary statistics in ( a ) (n, min, max, median, 25th and 75th percentiles, lower whisker, upper whisker): Nanopore-nanoMDBG (1006, 0, 28.47, 0.15, 0.04, 0.46, 0, 1.09); metaMDBG (549, 0, 28.07, 0.18, 0.05, 0.6, 0, 1.37); metaFlye (326, 0, 18.56, 0.13, 0.03, 0.39, 0, 0.92): HiFi-metaMDBG (1239, 0, 28.27, 0.14, 0.04, 0.41, 0, 0.96); hifiasm-meta (667, 0, 23.3, 0.15, 0.05, 0.445, 0, 1.03); metaFlye (362, 0, 20.41, 0.14, 0.04, 0.4, 0, 0.93).
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The top row presents results for Nanopore data, and the bottom row for HiFi data. a Contamination level in contigs longer than 1 Mbp. The percentage above each plot indicates the overall proportion of long contaminated contigs (with contamination over 5%). b Number of clipping events supported by at least 10 reads. c Number of regions over 1,000 bp with no apparent read coverage. d Proportion of predicted proteins which are ≥90% the length of their best-matching known protein in a <t>reference</t> database (from contigs with more than 10x coverage). In ( a ), results are aggregated across assemblies of the three data sets: Human Gut, <t>Zymo</t> Fecal Reference and Soil, but separated by both data set and assembler in b , c , and d . The boxplot elements are the median (horizontal bar), 25th and 75th percentiles (box limits Q1 and Q3), Q1-1.5*IQR and Q3+1.5*IQR (whiskers, IQR = Q3 − Q1) and outliers. Summary statistics in ( a ) (n, min, max, median, 25th and 75th percentiles, lower whisker, upper whisker): Nanopore-nanoMDBG (1006, 0, 28.47, 0.15, 0.04, 0.46, 0, 1.09); metaMDBG (549, 0, 28.07, 0.18, 0.05, 0.6, 0, 1.37); metaFlye (326, 0, 18.56, 0.13, 0.03, 0.39, 0, 0.92): HiFi-metaMDBG (1239, 0, 28.27, 0.14, 0.04, 0.41, 0, 0.96); hifiasm-meta (667, 0, 23.3, 0.15, 0.05, 0.445, 0, 1.03); metaFlye (362, 0, 20.41, 0.14, 0.04, 0.4, 0, 0.93).
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For each sequencing platform, filled points indicate the number of ASVs with an exact match to a theoretical ASV, while open points represent the total number of ASVs. For each primer set, the dotted line marks the number of theoretical ASVs based on the curated <t>Zmock</t> reference sequences trimmed to match the amplified regions. Identical subsampling depths were applied across all datasets, and the final point represents the maximum number of available reads.
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For each sequencing platform, filled points indicate the number of ASVs with an exact match to a theoretical ASV, while open points represent the total number of ASVs. For each primer set, the dotted line marks the number of theoretical ASVs based on the curated <t>Zmock</t> reference sequences trimmed to match the amplified regions. Identical subsampling depths were applied across all datasets, and the final point represents the maximum number of available reads.
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The top row presents results for Nanopore data, and the bottom row for HiFi data. a Contamination level in contigs longer than 1 Mbp. The percentage above each plot indicates the overall proportion of long contaminated contigs (with contamination over 5%). b Number of clipping events supported by at least 10 reads. c Number of regions over 1,000 bp with no apparent read coverage. d Proportion of predicted proteins which are ≥90% the length of their best-matching known protein in a reference database (from contigs with more than 10x coverage). In ( a ), results are aggregated across assemblies of the three data sets: Human Gut, Zymo Fecal Reference and Soil, but separated by both data set and assembler in b , c , and d . The boxplot elements are the median (horizontal bar), 25th and 75th percentiles (box limits Q1 and Q3), Q1-1.5*IQR and Q3+1.5*IQR (whiskers, IQR = Q3 − Q1) and outliers. Summary statistics in ( a ) (n, min, max, median, 25th and 75th percentiles, lower whisker, upper whisker): Nanopore-nanoMDBG (1006, 0, 28.47, 0.15, 0.04, 0.46, 0, 1.09); metaMDBG (549, 0, 28.07, 0.18, 0.05, 0.6, 0, 1.37); metaFlye (326, 0, 18.56, 0.13, 0.03, 0.39, 0, 0.92): HiFi-metaMDBG (1239, 0, 28.27, 0.14, 0.04, 0.41, 0, 0.96); hifiasm-meta (667, 0, 23.3, 0.15, 0.05, 0.445, 0, 1.03); metaFlye (362, 0, 20.41, 0.14, 0.04, 0.4, 0, 0.93).

Journal: Nature Communications

Article Title: High-quality metagenome assembly from nanopore reads with nanoMDBG

doi: 10.1038/s41467-026-69760-y

Figure Lengend Snippet: The top row presents results for Nanopore data, and the bottom row for HiFi data. a Contamination level in contigs longer than 1 Mbp. The percentage above each plot indicates the overall proportion of long contaminated contigs (with contamination over 5%). b Number of clipping events supported by at least 10 reads. c Number of regions over 1,000 bp with no apparent read coverage. d Proportion of predicted proteins which are ≥90% the length of their best-matching known protein in a reference database (from contigs with more than 10x coverage). In ( a ), results are aggregated across assemblies of the three data sets: Human Gut, Zymo Fecal Reference and Soil, but separated by both data set and assembler in b , c , and d . The boxplot elements are the median (horizontal bar), 25th and 75th percentiles (box limits Q1 and Q3), Q1-1.5*IQR and Q3+1.5*IQR (whiskers, IQR = Q3 − Q1) and outliers. Summary statistics in ( a ) (n, min, max, median, 25th and 75th percentiles, lower whisker, upper whisker): Nanopore-nanoMDBG (1006, 0, 28.47, 0.15, 0.04, 0.46, 0, 1.09); metaMDBG (549, 0, 28.07, 0.18, 0.05, 0.6, 0, 1.37); metaFlye (326, 0, 18.56, 0.13, 0.03, 0.39, 0, 0.92): HiFi-metaMDBG (1239, 0, 28.27, 0.14, 0.04, 0.41, 0, 0.96); hifiasm-meta (667, 0, 23.3, 0.15, 0.05, 0.445, 0, 1.03); metaFlye (362, 0, 20.41, 0.14, 0.04, 0.4, 0, 0.93).

Article Snippet: Zymo mock reference genomes are available at https://s3.amazonaws.com/zymo-files/BioPool/D6331.refseq.zip .

Techniques: Whisker Assay

For each sequencing platform, filled points indicate the number of ASVs with an exact match to a theoretical ASV, while open points represent the total number of ASVs. For each primer set, the dotted line marks the number of theoretical ASVs based on the curated Zmock reference sequences trimmed to match the amplified regions. Identical subsampling depths were applied across all datasets, and the final point represents the maximum number of available reads.

Journal: bioRxiv

Article Title: Nanopore sequencing reaches amplicon sequence variant (ASV) resolution

doi: 10.64898/2026.02.26.708165

Figure Lengend Snippet: For each sequencing platform, filled points indicate the number of ASVs with an exact match to a theoretical ASV, while open points represent the total number of ASVs. For each primer set, the dotted line marks the number of theoretical ASVs based on the curated Zmock reference sequences trimmed to match the amplified regions. Identical subsampling depths were applied across all datasets, and the final point represents the maximum number of available reads.

Article Snippet: We first evaluated the ASVs generated from both PacBio and ONT sequencing of the ZymoBIOMICS mock community (Zmock) (Cat. No. D6305, Zymo Research, USA), which contains eight bacteria and two fungal species ( Supplementary Table S1 ).

Techniques: Sequencing, Amplification