Runcer-Necromancer: a method to rescue data from an interrupted run on MGISEQ-2000 [version 2; peer review: 1 approved, 1 approved with reservations]

• Published in: F1000 research Vol. 10; p. 22
• Main Authors: Pavlova, Anna, Belova, Vera, Afasizhev, Robert, Bulusheva, Irina, Rebrikov, Denis, Korostin, Dmitriy
• Format: Journal Article
• Language: English
• Published: 2022
• Subjects: fastq merging; NGS; DNBSEQ-G400; Paired-end sequencing; MGISEQ-2000
• ISSN: 2046-1402; 2046-1402
• DOI: 10.12688/f1000research.27763.2

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 custom 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.