feat: Implement shifted reference to fix MAPQ0 due to identical sequence parts

scholl-lab / plasmicheck

Detect and quantify plasmid DNA contamination in sequencing data

MIT License

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Open berntpopp opened 3 months ago

berntpopp commented 3 months ago

Description: Develop a solution to handle MAPQ0 issues caused by identical sequence parts in the shifted reference, improving alignment accuracy.

Tasks:

Analyze the cause of MAPQ0 issues with identical sequence parts.
Implement a strategy to differentiate identical sequences in the shifted reference.
Validate the solution to ensure it resolves MAPQ0 issues.