ONT microbiome method benchmarking, Göttingen
73 samples from adults in Göttingen were used to benchmark swab, DNA extraction, library prep, and bioinformatics methods for complex microbiota sequencing on Oxford Nanopore, comparing 16S rRNA and metagenomic approaches. machine-written summary
73 samples · 73 runs · DE · Adult · 2021 · 74.8 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 292 sample values (age, country, location locality, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC8407471 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 73 | 100% | ||||
| country | 73 | 100% | 73 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 73 | 100% | 73 | |||
| age_at_collection_days | 73 | 100% | 73 | |||
| detailed_location | 73 | 100% | ||||
| location_locality | 73 | 100% | 73 |
- Comprehensive Wet-Bench and Bioinformatics Workflow for Complex Microbiota Using Oxford Nanopore Technologies. 2021 PMID 34427527 PMC8407471 own_data
Archive description
We present a comprehensive analysis pipeline with sampling, storage, DNA extraction, library preparation, and bioinformatical evaluation for complex microbiomes sequenced with Oxford nanopore Technologies (ONT). Our findings from the swabs and DNA extraction experiments indicate that methods, which were approved for NGS microbiome analysis cannot be simply adapted to ONT. We recommend using swabs and DNA extractions protocols with appropriate medium or extended washing steps. Both 16S rRNA and metagenomic sequencing achieved reliable and reproducible results. Still, the relatively high error rate of ONT sequences remains a bioinformatical challenge. Our benchmarking experiments reveal thresholds for analysis parameters which achieved excellent precision, recall and AUPR values.
How this project entered the registry
Classified as human gut / stool / oral cavity shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.57. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site sample.attr.host_body_site · “rectal mucosa (n=41/73)”
- body site sample.attr.host_body_site · “buccal mucosa (n=31/73)”
- life stage sample.attr.host_age · “30 (n=73/73)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA9926162 | age_at_collection_days | 10957.5 | R1 | 0.90 | sample.attr.host_age | 30 |
| SAMEA9926162 | country | DE | R1 | 0.90 | sample.attr.geo_loc_name | Stadt Gottingen |
| SAMEA9926162 | location_locality | Göttingen | R1 | 0.85 | biosample.attribute:geo_loc_name | Stadt Gottingen |
| SAMEA9926162 | subject_id | 3 | R1 | 0.85 | biosample.attribute:host_subject_id | 3 |
Sequencing
73 runs over 73 samples · mean 0.27 Gbp per run (median 74.8 Mbp, total 19.87 Gbp; 73 runs with a base count) · layout SINGLE 73 · platform OXFORD_NANOPORE 73 · models GridION (73) · 0% of runs with a Sandpiper profile · first public 2021-09-21 – 2021-09-25
Authors (0)
No author record.
Downloads
PRJEB47459.csv.gz (2.3 KB) · parquet (71.8 KB) — all 73 samples, every field with route and confidence · PRJEB47459_determinations.csv.gz (2.0 KB) — 292 evidence rows