How to measure viral abundance in competitive fitness assay with de novo assembly?
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.
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rezaeir75 •
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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.
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.