How to measure viral abundance in competitive fitness assay with de novo assembly?

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3.7 years ago

rezaeir75 ▴ 40

I want to perform a competitive fitness test to compare viral abundance between VSV strains which have different transgenes in them. I'm just starting to learn about de novo assembly and fitness assay. I wonder if you could give me a tutorial or guide to learn these methods and analysis procedures in detail to do my test. I found a paper close to what I'd like to do and It has used SPAdes for de novo assembly and BBmap for measuring the abundance. Please introduce me to a related tutorial web page or video for learning these tools.

Assembly rna-seq alignment genome • 609 views

ADD COMMENT • link 3.7 years ago by rezaeir75 ▴ 40

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BBMap is simple to use. There is extensive in-line help available. You can find a guide for BBMap here. BBTools are a collection of tools that do lots of things. A compilation of tool tips is in this thread on SeqAnswers.

SPAdes has good manual available online.

ADD REPLY • link 3.7 years ago by GenoMax 141k

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Thanks for your comment. Eventually I will read the docs for these tools. However, my primary reason for asking this question is to find a pipeline/workflow kind of tutorial/book/workshop for going through all the de novo assembly and measuring abundance for a sample dataset.

ADD REPLY • link 3.7 years ago by rezaeir75 ▴ 40

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