Comparative analysis of novel MGISEQ-2000 sequencing platform vs Illumina HiSeq 2500 for whole-genome sequencing

Korostin, Dmitriy; Kulemin, Nikolay A.; Наумов, В. А.; Belova, Vera; Kwon, Dmitriy; Gorbachev, A. Yu.

doi:10.1371/journal.pone.0230301

Cited by 63 publications

(49 citation statements)

References 20 publications

(35 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The overall sequencing quality was higher on the MGISEQ-2000 when compared to the BGISEQ-500, with more clean bases and clean reads produced. The sequencing technology implemented on each platform is the same -with the generation of a DNA Nanoball (DNB) and the cPAS method, where an oligonucleotide probe is added and attaches in combination to specific sites within the DNB [4,5]. Differences between the platforms may become clearer if longer read lengths are used (PE150) as read quality decreases over the entire read length.…”

Section: Discussionmentioning

confidence: 99%

“…MGI Tech Co.Ltd (MGI), a subsidiary of BGI, released two new sequencing instruments, namely the MGISEQ-2000 and MGISEQ-200, in October 2017. These sequencers rely on MGI's proprietary DNBseq TM technology and the combinatorial Probe-Anchor Synthesis (cPAS) method, an improvement of the combinatorial Probe-Anchor Ligation (cPAL) sequencing technology, first patented by Complete Genomics [4,5]. As described by Korostin et al, the MGI-SEQ2000 is a complete alternative to the Illumina platform for similar tasks, including whole genome sequencing (WGS) [4].…”

Section: Introductionmentioning

confidence: 99%

“…These sequencers rely on MGI's proprietary DNBseq TM technology and the combinatorial Probe-Anchor Synthesis (cPAS) method, an improvement of the combinatorial Probe-Anchor Ligation (cPAL) sequencing technology, first patented by Complete Genomics [4,5]. As described by Korostin et al, the MGI-SEQ2000 is a complete alternative to the Illumina platform for similar tasks, including whole genome sequencing (WGS) [4]. Importantly, the affordable pricing has made it possible to provide human WGS in settings with limited resources, such as South Africa.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Human Whole Genome Sequencing in South Africa

Glanzmann

Jooste

Ghoor

et al. 2020

Preprint

View full text Add to dashboard Cite

ABSTRACTThe advent and evolution of next generation sequencing has considerably impacted genomic research. Until recently, South African researchers were unable to access affordable platforms capable of human whole genome sequencing locally and DNA samples had to be exported. Here we report the whole genome sequences of the first six human DNA samples sequenced and analysed at the South African Medical Research Council’s Genomics Centre. We demonstrate that the data obtained is of high quality, with an average sequencing depth of 36.41, and that the output is comparable to data generated internationally on a similar platform. The Genomics Centre creates an environment where African researchers are able to access world class facilities, increasing local capacity to sequence whole genomes as well as store and analyse the data.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Human Whole Genome Sequencing in South Africa

Glanzmann

Jooste

Ghoor

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…It generates sequences in FASTQ format with quality scores based on a Phred-33 standard (equivalent to Illumina's NovaSeq system). Several studies have validated its sequencing quality by comparing its performance with that of Illumina generated sequence data from ancient DNA [24], whole-genome [25] and metagenome Fig. 1 Comparison of different strategies to access COI barcode using HTS platforms.…”

Section: Introductionmentioning

confidence: 99%

Efficient COI barcoding using high throughput single-end 400 bp sequencing

et al. 2020

View full text Add to dashboard Cite

Background Over the last decade, the rapid development of high-throughput sequencing platforms has accelerated species description and assisted morphological classification through DNA barcoding. However, the current high-throughput DNA barcoding methods cannot obtain full-length barcode sequences due to read length limitations (e.g. a maximum read length of 300 bp for the Illumina’s MiSeq system), or are hindered by a relatively high cost or low sequencing output (e.g. a maximum number of eight million reads per cell for the PacBio’s SEQUEL II system). Results Pooled cytochrome c oxidase subunit I (COI) barcodes from individual specimens were sequenced on the MGISEQ-2000 platform using the single-end 400 bp (SE400) module. We present a bioinformatic pipeline, HIFI-SE, that takes reads generated from the 5′ and 3′ ends of the COI barcode region and assembles them into full-length barcodes. HIFI-SE is written in Python and includes four function modules of filter, assign, assembly and taxonomy. We applied the HIFI-SE to a set of 845 samples (30 marine invertebrates, 815 insects) and delivered a total of 747 fully assembled COI barcodes as well as 70 Wolbachia and fungi symbionts. Compared to their corresponding Sanger sequences (72 sequences available), nearly all samples (71/72) were correctly and accurately assembled, including 46 samples that had a similarity score of 100% and 25 of ca. 99%. Conclusions The HIFI-SE pipeline represents an efficient way to produce standard full-length barcodes, while the reasonable cost and high sensitivity of our method can contribute considerably more DNA barcodes under the same budget. Our method thereby advances DNA-based species identification from diverse ecosystems and increases the number of relevant applications.

show abstract

“…MGISEQ is compatible with a wide range of reagents for sequencing in SE50, SE100, SE400, PE100, PE150, and PE200 modes. MGISEQ-2000 provides the quality of sequencing comparable with that of the Illumina platform [3][4][5][6].…”

Section: Introductionmentioning

confidence: 99%

Runcer-Necromancer: A Method To Rescue Data From An Interrupted Run On MGISEQ-2000

Pavlova

Belova

Afasizhev

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

During the sequencing process, problems can occur with any device including the MGISEQ-2000 (DNBSEQ-G400) platform. We encountered a power outage that resulted in a temporary shutdown of a sequencer in the middle of the run. Since barcode reading in MGISEQ-2000 takes place at the end of the run, it was impossible to use non-demultiplexed raw data. We decided to completely use up the same cartridge with reagents and flow cell loaded with DNB and started a new run in a shortened cus-tom mode. We figured out how the MGISEQ-2000 converts preliminary data in .cal format into .fastq files and wrote a script named Runcer-Necromacer for merging .fastq files based on the analysis of their headers (available online: https://github.com/genomecenter/runcer-necromancer ). Read merging proved to be possible because the MGISEQ-2000 flow cell has a patterned structure and each DNB has invariable coordinates on it, regardless of its position on the flow cell stage. We demonstrated the correctness of data merging by comparing sample analysis results with previously obtained .fastq files for them. Thus, we confirmed that it is possible to restart the device and save both parts of the interrupted run.

show abstract

Comparative analysis of novel MGISEQ-2000 sequencing platform vs Illumina HiSeq 2500 for whole-genome sequencing

Cited by 63 publications

References 20 publications

Human Whole Genome Sequencing in South Africa

Human Whole Genome Sequencing in South Africa

Efficient COI barcoding using high throughput single-end 400 bp sequencing

Runcer-Necromancer: A Method To Rescue Data From An Interrupted Run On MGISEQ-2000

Contact Info

Product

Resources

About