necessary to filter bac or host at the beginning?

allind / EukDetect

MIT License

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necessary to filter bac or host at the beginning? #16

Closed ifanlyn95 closed 3 years ago

ifanlyn95 commented 3 years ago

Hi, Abigail Lind. If I want to utilize EukDetect to align the raw metagenomic fastQ files containing the host or bacteria sequences. Is it necessary to filter the contamination at the beginning?

ifanlyn95 commented 3 years ago

Thank you for your works and looking for your replying. If my publication has been published, I would like to cite you.

allind commented 3 years ago

It depends on what the host is. If the host is a vertebrate animal such as human or a land plant, it's probably not necessary. If the host is something else, it might be contained in the database ot have a closely related species in the database, so I would recommend prefiltering

This work has been published - thanks for your interest. Please cite this paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-021-01015-y

ifanlyn95 commented 3 years ago

Received, I will check it and follow your suggestions. thank you very much.