Senabouth Anne, Andersen Stacey, Shi Qianyu, Shi Lei, Jiang Feng, Zhang Wenwei, Wing Kristof, Daniszewski Maciej, Lukowski Samuel W, Hung Sandy S C, Nguyen Quan, Fink Lynn, Beckhouse Anthony, Pébay Alice, Hewitt Alex W, Powell Joseph E
Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.
Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4067, Australia.
NAR Genom Bioinform. 2020 May 13;2(2):lqaa034. doi: 10.1093/nargab/lqaa034. eCollection 2020 Jun.
The libraries generated by high-throughput single cell RNA-sequencing (scRNA-seq) platforms such as the Chromium from 10× Genomics require considerable amounts of sequencing, typically due to the large number of cells. The ability to use these 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 generated on the 10× Genomics Chromium platform. Our results demonstrate a highly comparable performance between the NovaSeq 6000 and MGISEQ-2000 in sequencing quality, and the detection of genes, cell barcodes, Unique Molecular Identifiers. The performance of the NextSeq 500 was also similarly comparable to the MGISEQ-2000 based on the same metrics. Data generated by both sequencing platforms yielded similar analytical outcomes for general single-cell analysis. The performance of the NextSeq 500 and MGISEQ-2000 were also comparable for the deconvolution of multiplexed cell pools via variant calling, and detection of guide RNA (gRNA) from a pooled CRISPR single-cell screen. Our study provides a benchmark for high-capacity sequencing platforms applied to high-throughput scRNA-seq libraries.
由10×基因组学公司的Chromium等高通量单细胞RNA测序（scRNA-seq）平台生成的文库需要大量测序，这通常是由于细胞数量众多。利用这些数据解决生物学问题的能力直接受到序列数据质量的影响。在这里，我们使用在10×基因组学Chromium平台上生成的由超过70000个细胞组成的相同单细胞3'文库，比较了Illumina NextSeq 500和NovaSeq 6000与BGI MGISEQ-2000平台的性能。我们的结果表明，NovaSeq 6000和MGISEQ-2000在测序质量、基因检测、细胞条形码检测、独特分子标识符检测方面具有高度可比的性能。基于相同指标，NextSeq 500的性能与MGISEQ-2000也同样具有可比性。两个测序平台生成的数据在一般单细胞分析中产生了相似的分析结果。NextSeq 500和MGISEQ-2000在通过变异检测对多重细胞池进行解卷积以及从汇集的CRISPR单细胞筛选中检测引导RNA（gRNA）方面的性能也具有可比性。我们的研究为应用于高通量scRNA-seq文库的高容量测序平台提供了一个基准。
