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Comparative performance of the BGI and Illumina sequencing technology for single-cell RNA-sequencing

Anne Senabouth, Stacey Andersen, Qianyu Shi, Lei Shi, Feng Jiang, Wenwei Zhang, Kristof Wing, Maciej Daniszewski, Samuel W Lukowski, Sandy SC Hung, Quan Nguyen, Lynn Fink, Ant Beckhouse, Alice Pébay, Alex W Hewitt, Joseph E Powell
doi: https://doi.org/10.1101/552588
Anne Senabouth
1Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney
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Stacey Andersen
2Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane
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Qianyu Shi
3MGI, BGI-Shenzhen, Shenzhen 518083, China
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Lei Shi
3MGI, BGI-Shenzhen, Shenzhen 518083, China
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Feng Jiang
3MGI, BGI-Shenzhen, Shenzhen 518083, China
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Wenwei Zhang
4BGI-Shenzhen, Shenzhen 518083, China
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Kristof Wing
5Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Hobart
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Maciej Daniszewski
6Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, Melbourne
7Department of Surgery, The University of Melbourne, Parkville, Melbourne
8Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne
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Samuel W Lukowski
2Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane
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Sandy SC Hung
8Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne
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Quan Nguyen
2Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane
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Lynn Fink
9BGI Australia, 300 Herston Rd, Brisbane
10Diamantina Institute, The University of Queensland, Woolloongabba, Brisbane
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Ant Beckhouse
9BGI Australia, 300 Herston Rd, Brisbane
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Alice Pébay
6Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, Melbourne
7Department of Surgery, The University of Melbourne, Parkville, Melbourne
8Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne
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Alex W Hewitt
5Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Hobart
11Centre for Eye Research Australia, The University of Melbourne, Royal Victorian Eye & Ear Hospital, Melbourne
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Joseph E Powell
1Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney
12St Vincent’s Clinical School, University of New South Wales, Sydney
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  • For correspondence: j.powell@garvan.org.au
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Abstract

The libraries generated by high-throughput single cell RNA-sequencing platforms such as the Chromium from 10x Genomics require considerable amounts of sequencing, typically due to the large number of cells. The ability to use this data to address biological questions is directly impacted by the quality of the sequence data. Here we have compared the performance of the Illumina NextSeq 500 and NovaSeq 6000 against the BGI MGISEQ-2000 platform using identical Single Cell 3’ libraries consisting of over 70,000 cells. Our results demonstrate a highly comparable performance between the NovaSeq 6000 and MGISEQ-2000 in sequencing quality, and cell, UMI, and gene detection. However, compared with the NextSeq 500, the MGISEQ-2000 platform performs consistently better, identifying more cells, genes, and UMIs at equalised read depth. We were able to call an additional 1,065,659 SNPs from sequence data generated by the BGI platform, enabling an additional 14% of cells to be assigned to the correct donor from a multiplexed library. However, both the NextSeq 500 and MGISEQ-2000 detected similar frequencies of gRNAs from a pooled CRISPR single cell screen. Our study provides a benchmark for high capacity sequencing platforms applied to high-throughput single cell RNA-seq libraries.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted February 24, 2019.
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Comparative performance of the BGI and Illumina sequencing technology for single-cell RNA-sequencing
Anne Senabouth, Stacey Andersen, Qianyu Shi, Lei Shi, Feng Jiang, Wenwei Zhang, Kristof Wing, Maciej Daniszewski, Samuel W Lukowski, Sandy SC Hung, Quan Nguyen, Lynn Fink, Ant Beckhouse, Alice Pébay, Alex W Hewitt, Joseph E Powell
bioRxiv 552588; doi: https://doi.org/10.1101/552588
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Comparative performance of the BGI and Illumina sequencing technology for single-cell RNA-sequencing
Anne Senabouth, Stacey Andersen, Qianyu Shi, Lei Shi, Feng Jiang, Wenwei Zhang, Kristof Wing, Maciej Daniszewski, Samuel W Lukowski, Sandy SC Hung, Quan Nguyen, Lynn Fink, Ant Beckhouse, Alice Pébay, Alex W Hewitt, Joseph E Powell
bioRxiv 552588; doi: https://doi.org/10.1101/552588

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