University Of Tasmania
152827 - Comparative performance of the BGI and Illumina sequencing.pdf (4.78 MB)

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

Download (4.78 MB)
journal contribution
posted on 2023-05-21, 12:55 authored by Senabouth, A, Andersen, S, Shi, Q, Shi, L, Jiang, F, Zhang, W, Kristof WingKristof Wing, Daniszewski, M, Lukowski, SW, Hung, SSC, Fink, L, Beckhouse, A, Pebay, A, Alexander HewittAlexander Hewitt, Powell, JE
The libraries generated by high-throughput single cell RNA-sequencing (scRNA-seq) 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 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 10x 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.


Publication title

NAR Genomics and Bioinformatics






Tasmanian School of Medicine


Oxford University Press

Place of publication


Rights statement

Copyright 2020 The Authors. Licensed under Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)

Repository Status

  • Open

Socio-economic Objectives

Diagnosis of human diseases and conditions

Usage metrics

    University Of Tasmania