Questions about read coverage and breadth filtration.

MrOlm / inStrain

Bioinformatics program inStrain

MIT License

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Questions about read coverage and breadth filtration. #179

Open ChenTianYi99 opened 3 months ago

ChenTianYi99 commented 3 months ago

Hi, I want to analyze viral populations with >10× average read depth coverage and >70% length of genome covered for microdiversity analyses. I wonder if i should set MIN_COV to 10 and filter by "breadth" in scaffold_info.tsv (or set other relevant parameters).

Thanks in advance.

MrOlm commented 3 months ago

Hi @ChenTianYi99 - if I were you I would run with default parameters, then filter the scaffold_info.tsv to coverage > 10 and breadth > 0.7. No need to adjust the MIN_COV when running the program.

Best, Matt