Runcer-Necromancer

Runcer-Necromancer recovers sequencing data from interrupted MGISEQ-2000 (DNBSEQ-G400) runs by converting partial .cal-derived reads into .fastq and merging them using patterned flow cell/DNA Nanoball coordinates to restore reads lost when barcode reading did not occur.

Key Features:

• Data recovery from interrupted runs: Enables continuation of interrupted runs by reusing the same reagent cartridge and flow cell in a shortened custom mode to recover data when barcode reading was not completed.
• Conversion and merging of data formats: Processes preliminary .cal files, converts them into .fastq using a custom script, and merges resulting .fastq files by analyzing read headers to combine reads from different run segments.
• Patterned flow cell utilization: Leverages the MGISEQ-2000 patterned flow cell with invariant coordinates for each DNA Nanoball (DNB) to accurately match and merge reads across interrupted runs.
• Validation and verification: Validates merged data by comparing analysis results with previously obtained complete .fastq datasets to confirm accuracy.

Scientific Applications:

• Genomic research continuity: Minimizes data loss and reduces the need for costly re-runs in projects where sequencing continuity is critical.
• Whole-genome sequencing: Recovers interrupted whole-genome sequencing runs to preserve coverage and read integrity for downstream analyses.
• Transcriptomics and metagenomics: Restores interrupted transcriptomic and metagenomic sequencing datasets to enable accurate expression profiling and community composition analyses.

Methodology:

Preliminary .cal files are converted into .fastq using a custom script; .fastq headers are analyzed to merge reads from different segments of the interrupted run; merged data are validated by comparison to previously obtained complete .fastq datasets.