BGISEQ-500 vs Illumina metagenomics, healthy adults, Sweden
Cross-sectional study of 20 fecal samples from healthy adults in Sweden, comparing intra- and inter-platform reproducibility of metagenomic shotgun sequencing between the BGISEQ-500 and Illumina HiSeq platforms. machine-written summary
20 samples · 76 runs · SE · Age unknown · 2017 · 14.47 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 100 sample values (collection date, country, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 80 sample values (antibiotic exposure, health condition, health condition detail, location locality) · PMC5848809 |
| ○ 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 |
Genera, mean relative abundance over 20 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 20 | 100% | ||||
| country | 20 | 100% | 20 | |||
| health_condition | 20 | 100% | 20 | |||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 20 | 100% | 20 | |||
| collection_date | 20 | 100% | 20 | |||
| detailed_location | 20 | 100% | ||||
| health_condition_detail | 20 | 100% | 20 | |||
| latitude | 20 | 100% | 20 | |||
| location_locality | 20 | 100% | 20 | |||
| location_region | 20 | 100% | 20 | |||
| longitude | 20 | 100% | 20 |
- Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing. 2018 PMID 29293960 PMC5848809 own_data
Archive description
BGISEQ-500 is a recently launched cPAS-based desktop sequencer, which has been used for RNA-seq and whole-genome sequencing. However, the performance of this high-throughput sequencing platform for metagenomic shotgun sequencing has not yet been evaluated.In this study, we generated a BGISEQ-500 metagenomic dataset from 20 healthy individuals including 8 sequencing replicates and 8 library replicates. By an in-house-developed overall-accuracy quality control method, BGISEQ-500 produced an average of 82.45 million high quality reads (96. 06% of raw reads) per sample with 90.56% of bases scoring Q30 and above. Quantitative analyses revealed extremely high reproducibility between BGISEQ-500 intra-platform replicates. Furthermore, we assessed the inter-platform variation using 20 pairwise cross-platform replicates on BGISEQ-500 and Illumina HiSeq 2000 and demonstrated a high consistency between platforms. Only 11,354 (3.25%) genes showed reproducible significant differences in relative abundance between platforms, with a bias towards genes with higher GC content being enriched on the HiSeq 2000 platform.Our results demonstrate excellent intra-platform stability and inter-platform consistency for metagenomic data using the BGISEQ-500 platform validating the applicability of this new sequencing platform for quantitative metagenomic studies. We hope that you find our data and manuscript of general interest and sufficient quality to be considered for publication in GigaScience.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.60. Assay shotgun_dna.
- host study.description · “20 healthy individuals”
- host run.scientific_name · “human gut metagenome”
- body site sample.attr.environment_biome · “human gut (n=20/20)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA104224051 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | no antibiotic treatment for at least 60 days |
| SAMEA104224051 | collection_date | 2013 | R1 | 0.90 | biosample.attribute:collection_date | 2013 |
| SAMEA104224051 | country | SE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Sweden |
| SAMEA104224051 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | Twenty Swedish healthy adults |
| SAMEA104224051 | health_condition_detail | healthy adults, no diagnosed GI problems | R3 | 0.70 | paper.fulltext.methods | Twenty Swedish healthy adults |
| SAMEA104224051 | latitude | 59.3200 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 59.32 18.06 |
| SAMEA104224051 | location_locality | Stockholm | R3 | 0.70 | paper.fulltext.methods | living in the Stockholm regional area |
| SAMEA104224051 | location_region | Stockholm | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 59.32 18.06 |
| SAMEA104224051 | longitude | 18.0600 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 59.32 18.06 |
Sequencing
76 runs over 20 samples · mean 4.81 Gbp per run (median 4.16 Gbp, total 365.80 Gbp; 76 runs with a base count) · layout SINGLE 76 · platform ILLUMINA 40, BGISEQ 36 · models BGISEQ-500 (36), Illumina HiSeq 2000 (20), Illumina HiSeq 4000 (20) · 50% of runs with a Sandpiper profile · first public 2017-12-13
Authors (20)
Fang C first · Zhong H · Lin Y · Chen B · Han M · Ren H · Lu H · Luber JM · Xia M · Li W · Stein S · Xu X · Zhang W · Drmanac R · Wang J · Yang H · Hammarström L · Kostic AD · Kristiansen K · Li J last
Downloads
PRJEB35961.csv.gz (1.4 KB) · parquet (70.8 KB) — all 20 samples, every field with route and confidence · PRJEB35961_determinations.csv.gz (1.7 KB) — 180 evidence rows