Journal: mSystems

Article Title: Comprehensive Wet-Bench and Bioinformatics Workflow for Complex Microbiota Using Oxford Nanopore Technologies

doi: 10.1128/mSystems.00750-21

Figure Lengend Snippet: Impact of eating and drinking on the buccal microbiome. (a) Experimental design. Four healthy nonvegetarian volunteers followed the protocol for 2 days. (b) Unweighted UniFrac distance ordinated with principal coordinate analysis showing the beta diversity at species level. Squares display the buccal swabs in the morning before eating (baseline), circles are the samples after eating (5 min, 30 min, and 240 min), whereas stars represent samples after drinking (5 min, 30 min, and 240 min). Samples were rarefied to 9,000 reads/sample.

Article Snippet: As a positive control, a gut mock community was purchased from ZymoBIOMICS gut microbiome standard (Zymo Research), extracted, and sequenced alongside swab samples.

Techniques:

Journal: BMC Bioinformatics

Article Title: Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets

doi: 10.1186/s12859-022-05103-0

Figure Lengend Snippet: Description of the publicly available mock community datasets used for this experiment

Article Snippet: Different mock communities were available for PacBio HiFi (ATCC MSA-1003, Zymo D6331) and ONT (Zymo D6300), which prevents a direct comparison of detection metrics (precision, recall, and F-scores) and detection limits across sequencing technologies.

Techniques:

Journal: BMC Bioinformatics

Article Title: Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets

doi: 10.1186/s12859-022-05103-0

Figure Lengend Snippet: Overview of taxonomic profiling methods used in this experiment

Article Snippet: Different mock communities were available for PacBio HiFi (ATCC MSA-1003, Zymo D6331) and ONT (Zymo D6300), which prevents a direct comparison of detection metrics (precision, recall, and F-scores) and detection limits across sequencing technologies.

Techniques:

Journal: BMC Bioinformatics

Article Title: Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets

doi: 10.1186/s12859-022-05103-0

Figure Lengend Snippet: Minimum detection thresholds used to score the presence/absence of mock community taxa at the species or genus level

Article Snippet: Different mock communities were available for PacBio HiFi (ATCC MSA-1003, Zymo D6331) and ONT (Zymo D6300), which prevents a direct comparison of detection metrics (precision, recall, and F-scores) and detection limits across sequencing technologies.

Techniques:

Journal: BMC Bioinformatics

Article Title: Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets

doi: 10.1186/s12859-022-05103-0

Figure Lengend Snippet: Read utilization for A HiFi ATCC MSA-1003, B HiFi Zymo D6331, C ONT R10 Zymo D6300, and (D) ONT Q20 Zymo D6300. The stacked barplots show the total percent of reads that were assigned to taxonomy. Different colors show the percentage of reads assigned to specific taxonomic ranks

Article Snippet: Different mock communities were available for PacBio HiFi (ATCC MSA-1003, Zymo D6331) and ONT (Zymo D6300), which prevents a direct comparison of detection metrics (precision, recall, and F-scores) and detection limits across sequencing technologies.

Techniques:

Journal: BMC Bioinformatics

Article Title: Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets

doi: 10.1186/s12859-022-05103-0

Figure Lengend Snippet: Precision, recall and F-scores for the species-level analysis based on a minimum threshold of 0.001% of the total reads for A HiFi ATCC MSA-1003, B HiFi Zymo D6331, C ONT R10 Zymo D6300, and D ONT Q20 Zymo D6300

Article Snippet: Different mock communities were available for PacBio HiFi (ATCC MSA-1003, Zymo D6331) and ONT (Zymo D6300), which prevents a direct comparison of detection metrics (precision, recall, and F-scores) and detection limits across sequencing technologies.

Techniques:

Journal: BMC Bioinformatics

Article Title: Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets

doi: 10.1186/s12859-022-05103-0

Figure Lengend Snippet: Precision, recall and F-scores for the genus-level analysis based on a minimum threshold of 0.001% of the total reads for A HiFi ATCC MSA-1003, B HiFi Zymo D6331, C ONT R10 Zymo D6300, and D ONT Q20 Zymo D6300

Article Snippet: Different mock communities were available for PacBio HiFi (ATCC MSA-1003, Zymo D6331) and ONT (Zymo D6300), which prevents a direct comparison of detection metrics (precision, recall, and F-scores) and detection limits across sequencing technologies.

Techniques:

Journal: BMC Bioinformatics

Article Title: Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets

doi: 10.1186/s12859-022-05103-0

Figure Lengend Snippet: Species-level detection results based on the minimum 0.001% of total reads threshold

Article Snippet: Different mock communities were available for PacBio HiFi (ATCC MSA-1003, Zymo D6331) and ONT (Zymo D6300), which prevents a direct comparison of detection metrics (precision, recall, and F-scores) and detection limits across sequencing technologies.

Techniques:

Journal: BMC Bioinformatics

Article Title: Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets

doi: 10.1186/s12859-022-05103-0

Figure Lengend Snippet: Species-level relative abundance estimates for A HiFi ATCC MSA-1003, B HiFi Zymo D6331, C ONT R10 Zymo D6300, and D ONT Q20 Zymo D6300. The theoretical distributions are shown on the left and are based on the manufacturer’s specifications. The read counts for all species-level false positives were grouped in a category labeled ‘Other’. For HiFi Zymo D6331, all species assignments within the genera Prevotella and Veillonella were counted towards Prevotella corporis and Veillonella rogosae , due to the absence of these species from several databases (see " " Section). Asterisks signify methods that failed the chi-squared goodness of fit test (e.g., the abundance estimates were significantly different from the theoretical values)

Article Snippet: Different mock communities were available for PacBio HiFi (ATCC MSA-1003, Zymo D6331) and ONT (Zymo D6300), which prevents a direct comparison of detection metrics (precision, recall, and F-scores) and detection limits across sequencing technologies.

Techniques: Labeling

Journal: BMC Bioinformatics

Article Title: Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets

doi: 10.1186/s12859-022-05103-0

Figure Lengend Snippet: Genus-level relative abundance estimates for A HiFi ATCC MSA-1003, B HiFi Zymo D6331, C ONT R10 Zymo D6300, and D ONT Q20 Zymo D6300. The theoretical distributions are shown on the left and are based on the manufacturer’s specifications. The read counts for all genus-level false positives were grouped in a category labeled ‘Other’. Asterisks signify methods that failed the chi-squared goodness of fit test (e.g., the abundance estimates were significantly different from the theoretical values)

Article Snippet: Different mock communities were available for PacBio HiFi (ATCC MSA-1003, Zymo D6331) and ONT (Zymo D6300), which prevents a direct comparison of detection metrics (precision, recall, and F-scores) and detection limits across sequencing technologies.

Techniques: Labeling