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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 genome assembly.

Note: I know that I should read the documentation on SPAdes and 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 aligner documentation.

cross-posted in biostars

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    $\begingroup$ Discussed already at Biostars. $\endgroup$ – ATpoint Aug 16 '20 at 21:27
  • $\begingroup$ biostars.org/p/455717 $\endgroup$ – Ram RS Aug 16 '20 at 22:04
  • $\begingroup$ @ATpoint why is that a valid reason to close? The internet is not non-redundant $\endgroup$ – Chris_Rands Aug 17 '20 at 15:00
  • $\begingroup$ It is commonly considered bad practice to cross-post (especially without indcating it) since it keeps members in both communities busy and spreads information across two threads. It is more productive to have things limited to one thread both in terms of avoiding double-effort and having information concentrated. $\endgroup$ – ATpoint Aug 17 '20 at 21:18
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    $\begingroup$ Thanks for your comment. But as you see in the post, I had indicated the cross-posting and its link from the first day that the post was submitted, both here and in biostar page. $\endgroup$ – Reza Rezaei Aug 18 '20 at 2:08

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