Modifications needed to assemble Influenza C genomes?

peterk87 / nf-flu

Influenza genome analysis Nextflow workflow

MIT License

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Modifications needed to assemble Influenza C genomes? #20

Open hkunerth opened 4 weeks ago

hkunerth commented 4 weeks ago

Research

[X] I have searched the documentation and previously asked questions.

Question about nf-flu

I've been successful in using NF-flu on flu A nd B sequencing data, but just got a request to assemble data from flu C. Do you know what the current limitations are in terms of working with flu C data and whether it would be possible to modify the pipeline accordingly?

peterk87 commented 4 weeks ago

Hi @hkunerth it's great to hear that the pipeline works for IAV and IBV. We've yet to sequence and analyze flu C in our lab. It's not something we've ever encountered, but IRMA, which this pipeline uses, should be able to generate a good quality assembly for flu C and other atypical influenza.

hkunerth commented 4 weeks ago

Sounds good! If we get things working for Flu C I'll let you know! Thanks!