I have sequencing data of a few samples of a
DNA genome virus. I'd like to learn
de novo assembly of the
short reads, making scaffolds from it, and then
counting the abundance of each strain in the data. I heard about
SPAdes as a good choice for these kinds of very short genomes. and also
BBmap for statistics related to contigs.
I am a complete newbie in everything related to de novo assembly. So, I wonder if you could recommend some good
courses/tutorials/papers for learning all the steps, including units, special vocabularies, analysis steps, and everything else.
I have some experience with analyzing
RNA-seq and also
small RNA-seq data. I learned these two using free online resources, however, it is very hard to find even one full workflow post/paper on
Note: I know that I should read the documentation on
BBmap and I will. However, I'd like to first get to a good idea of what are the steps, test it on some sample data, and then go through learning different tools. So, it is like saying that I need to learn RNA-seq analysis not read a particular
cross-posted in bioinformatics.stackexchange.