Supporting data for "Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing"

Dataset type: Software, Genomic
Data released on December 20, 2017

Fang C; 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 (2017): Supporting data for "Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing" GigaScience Database. http://dx.doi.org/10.5524/100395

DOI10.5524/100395

More extensive use of metagenomic shotgun sequencing in microbiome research relies on the development of high-throughput, cost-effective sequencing. Here we present a comprehensive evaluation of the performance of the new high-throughput sequencing platform BGISEQ-500 for metagenomic shotgun sequencing and compare its performance with that of two Illumina platforms.
Using fecal samples from 20 healthy individuals we evaluated the intra-platform reproducibility for metagenomic sequencing on the BGISEQ-500 platform in a setup comprising 8 library replicates and 8 sequencing replicates. Cross-platform consistency, was evaluated by comparing 20 pairwise replicates on the BGISEQ-500 platform versus the Illumina HiSeq 2000 platform and the Illumina HiSeq 4000 platform. In addition, we compared the performance of the two Illumina platforms against each other.
By a newly developed overall accuracy quality control method, 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 was obtained using the BGISEQ-500 platform. Quantitative analyses revealed extremely high reproducibility between BGISEQ-500 intra-platform replicates. Cross-platform replicates differed slightly more than intra-platform replicates, yet a high consistency was observed. Only a low percentage (2.02% -3.25%) of genes exhibited significant differences in relative abundance comparing the BGISEQ-500 and HiSeq platforms, with a bias towards genes with higher GC content being enriched on the HiSeq platforms.
Our study provides the first set of performance metrics for human gut metagenomic sequencing data using BGISEQ-500. The high accuracy and technical reproducibility confirm the applicability of the new platform for metagenomic studies, though caution is still warranted when combining metagenomic data from different platforms.

Additional details

Read the peer-reviewed publication(s):

Fang, C., Zhong, H., Lin, Y., Chen, B., Han, M., Ren, H., … Li, J. (2017). Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing. GigaScience, 7(3). doi:10.1093/gigascience/gix133

Accessions (data included in GigaDB):

BioProject: PRJEB35961





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
S01408170Human gut metagenome human gut metagenome Description:DNA extracted from fecal sample of hea...
Alternative accession-SRA Sample:ERS1883069
Alternative accession-BioSample:SAMEA104224051
...
+
S02408170Human gut metagenome human gut metagenome Description:DNA extracted from fecal sample of hea...
Alternative accession-SRA Sample:ERS1883070
Alternative accession-BioSample:SAMEA104224052
...
+
S03408170Human gut metagenome human gut metagenome Description:DNA extracted from fecal sample of hea...
Alternative accession-SRA Sample:ERS1883071
Alternative accession-BioSample:SAMEA104224053
...
+
S04408170Human gut metagenome human gut metagenome Description:DNA extracted from fecal sample of hea...
Alternative accession-SRA Sample:ERS1883072
Alternative accession-BioSample:SAMEA104224054
...
+
S05408170Human gut metagenome human gut metagenome Description:DNA extracted from fecal sample of hea...
Alternative accession-SRA Sample:ERS1883073
Alternative accession-BioSample:SAMEA104224055
...
+
S06408170Human gut metagenome human gut metagenome Description:DNA extracted from fecal sample of hea...
Alternative accession-SRA Sample:ERS1883074
Alternative accession-BioSample:SAMEA104224056
...
+
S07408170Human gut metagenome human gut metagenome Description:DNA extracted from fecal sample of hea...
Alternative accession-SRA Sample:ERS1883075
Alternative accession-BioSample:SAMEA104224057
...
+
S08408170Human gut metagenome human gut metagenome Description:DNA extracted from fecal sample of hea...
Alternative accession-SRA Sample:ERS1883076
Alternative accession-BioSample:SAMEA104224058
...
+
S09408170Human gut metagenome human gut metagenome Description:DNA extracted from fecal sample of hea...
Alternative accession-SRA Sample:ERS1883077
Alternative accession-BioSample:SAMEA104224059
...
+
S10408170Human gut metagenome human gut metagenome Description:DNA extracted from fecal sample of hea...
Alternative accession-SRA Sample:ERS1883078
Alternative accession-BioSample:SAMEA104224060
...
+
Displaying 1-10 of 20 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Tabular dataCSV117.64 KB2017-12-15
Packagearchive693.22 KB2017-12-15
Packagearchive1.98 GB2017-12-15
Tabular dataCSV8.22 KB2017-12-15
ScriptUNKNOWN2.04 KB2017-12-15
ScriptR0.95 KB2017-12-15
Tabular dataCSV1.71 KB2017-12-15
Tabular dataUNKNOWN3.34 KB2017-12-15
ScriptPerl0.47 KB2017-12-15
RdataUNKNOWN0.7 KB2017-12-15
Displaying 1-10 of 113 File(s).
Funding body Awardee Award ID Comments
National Key Research and Development Program of China J Li 2017YFC0909700
National Natural Science Foundation of China J Li 31601073
Shenzhen Municipal Government of China J Li JSGG20160229172752028
Shenzhen Municipal Government of China J Li CXB201108250098A
American Diabetes Association AD Kostic #1-17-INI-13 Pathway Award
Richard and Susan Smith Family Foundation AD Kostic
National Human Genome Research Institute AD Kostic HG002295
National Institute of General Medical Sciences AD Kostic GM074897
Date Action
December 20, 2017 Dataset publish
December 20, 2017 Description updated from : More extensive use of metagenomic shotgun sequencing in microbiome research relies on the development of high-throughput, cost-effective sequencing. Here we present a comprehensive evaluation of the performance of the new high-throughput sequencing platform BGISEQ-500 for metagenomic shotgun sequencing and compare its performance with that of two Illumina platforms. Using fecal samples from 20 healthy individuals we evaluated the intra-platform reproducibility for metagenomic sequencing on the BGISEQ-500 platform in a setup comprising 8 library replicates and 8 sequencing replicates. Cross-platform consistency, was evaluated by comparing 20 pairwise replicates on the BGISEQ-500 platform versus the Illumina HiSeq 2000 platform and the Illumina HiSeq 4000 platform. In addition, we compared the performance of the two Illumina platforms against each other. By a newly developed overall accuracy quality control method, 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 was obtained using the BGISEQ-500 platform. Quantitative analyses revealed extremely high reproducibility between BGISEQ-500 intra-platform replicates. Cross-platform replicates differed slightly more than intra-platform replicates, yet a high consistency was observed. Only a low percentage (2.02% -3.25%) of genes exhibited significant differences in relative abundance comparing the BGISEQ-500 and HiSeq platforms, with a bias towards genes with higher GC content being enriched on the HiSeq platforms. Our study provides the first set of performance metrics for human gut metagenomic sequencing data using BGISEQ-500. The high accuracy and technical reproducibility confirm the applicability of the new platform for metagenomic studies, though caution is still warranted when combining metagenomic data from different platforms.
December 20, 2017 File 3randomReads.csv updated
December 20, 2017 File cordat.positive.csv updated
December 20, 2017 File Both.n56.report.csv updated
December 20, 2017 File ready.csv updated
December 20, 2017 File tmpIO updated
December 20, 2017 File tmpIO updated
December 20, 2017 File tmpIO updated
December 20, 2017 File doGrid.pl updated
December 20, 2017 File simulate.read.gene.qq.plot.R updated
December 20, 2017 File simulate.read.RA.qq.plot.R updated
December 20, 2017 File transProf.pl updated
December 20, 2017 File cor.20M.ab10.R updated
December 20, 2017 File cutoff.pl updated
January 9, 2018 Manuscript Link added : 10.1093/gigascience/gix133