I have sequencing data of a few samples of a DNA virus.
I'd like to learn de novo assembly of 'short read' data, to construct a scaffold and then count 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 new to de novo assembly could you also recommend introductory material? For example a full workflow post/paper on genome assembly.
I have some experience with RNA-seq and small RNA-seq data.
Note: I am seeking an overview and test data prior reading Spades and BBmap manuals. Thus I need to learn RNA-seq analysis rather than a
cross-posted in biostars