Runcer-Necromancer: a method to rescue data from an interrupted run on MGISEQ-2000
| Autor: | Irina Bulusheva, Anna Pavlova, Vera Belova, Dmitriy Korostin, Robert Afasizhev, Denis V. Rebrikov |
|---|---|
| Rok vydání: | 2022 |
| Předmět: |
0301 basic medicine
FASTQ format Correctness General Immunology and Microbiology Computer science Reading (computer) Sample (material) Process (computing) Flow cell General Medicine Barcode computer.software_genre General Biochemistry Genetics and Molecular Biology law.invention 03 medical and health sciences 030104 developmental biology 0302 clinical medicine Mode (computer interface) law Operating system General Pharmacology Toxicology and Pharmaceutics computer 030217 neurology & neurosurgery |
| Zdroj: | F1000Research. 10:22 |
| ISSN: | 2046-1402 |
| DOI: | 10.12688/f1000research.27763.2 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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