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bede / hostile

Precise host read removal
MIT License
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Suitable for metatranscriptomics? #31

Closed ym2877 closed 7 months ago

ym2877 commented 11 months ago

Hi! I was just wondering if this would be suitable for removing human contaminants from metatranscriptomics (RNA-seq)? And, if so, would you recommend using the default human-t2t or the human-t2t + argos985?

Thank you!

bede commented 11 months ago

Hi Yoli, this sounds fine in principle, can you tell me more about your dataset? Presumably your metatranscriptomes are bacterial? How long are your reads? Happy to discuss here or via email. If bacterial, I would recommend human-t2t-hla-argos985. I will also be releasing a reference masked against viral genomes soon (https://github.com/bede/hostile/issues/30).

Bede

bede commented 10 months ago

In case of interest, I've just added a human index masked agains bacterial, viral and phage genomes: human-t2t-hla.argos-bacteria-985_rs-viral-202401_ml-phage-202401 . More info can be found in the readme.

bede commented 7 months ago

Closing due to inactivity