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Data released on December 20, 2017

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

Fang, C; Zhong, H; Lin, Y; Chen, B; Han, M; Ren, H; Lu, H; Luber, J, M; Xia, M; Li, W; Stein, S; Xu, X; Zhang, W; Drmanac, R; Wang, J; Yang, H; Hammarström, L; Kostic, A, D; 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 RIS BibTeX Text

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.

Contact Submitter

Related manuscripts:

doi:10.1093/gigascience/gix133

Accessions (data included in GigaDB):

BioProject: PRJEB35961

Genomic, Software

http://gigadb.org/images/data/cropped/100395.png

Funding:

  • Funding body - National Key Research and Development Program of China
  • Award ID - 2017YFC0909700
  • Funding body - National Natural Science Foundation of China
  • Award ID - 31601073
  • Funding body - Shenzhen Municipal Government of China
  • Location - China
  • Award ID - JSGG20160229172752028
  • Funding body - Shenzhen Municipal Government of China
  • Location - China
  • Award ID - CXB201108250098A
  • Funding body - American Diabetes Association
  • Award ID - #1-17-INI-13
  • Comment - Pathway Award
  • Funding body - Richard and Susan Smith Family Foundation
  • Funding body - National Human Genome Research Institute
  • Award ID - HG002295
  • Funding body - National Institute of General Medical Sciences
  • Award ID - GM074897

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

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
...
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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).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile 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).

History:

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