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MrOlm / inStrain

Bioinformatics program inStrain
MIT License
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InStrain for PacBio longreads #104

Open DanielSpari opened 2 years ago

DanielSpari commented 2 years ago

Hi,

I am quite new to the field of metagenomic sequencing and we are starting a new project in our lab and want to use your pipeline to determine if some sub-strains emerge or abolish over time. Originally we wanted to do this using illumina sequencing but now we are also considering PacBio long-read sequencing. Has this ever been done so far, this should work as well, right?

Cheers Dani

MrOlm commented 2 years ago

Hi Dani,

Right now inStrain has an issue where it's a little difficult to update the read error-rate model, meaning using more error-prone reads can lead it being a bit promiscuous during SNV calling. It's still possible to use long-reads with a bit of work, though, and I hope to release an update soon that will make changing the expected read error-rate easy.

Best, Matt

cifuj commented 2 years ago

Would this also be an issue for HiFi PacBio reads?

MrOlm commented 2 years ago

It depends on the fidelity of the reads- if you have ~Q30 base scores, it won't be a problem