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 aligner.

cross-posted in biostars

  • 2
    $\begingroup$ Discussed already at Biostars. $\endgroup$
    – ATpoint
    Aug 16, 2020 at 21:27
  • $\begingroup$ biostars.org/p/455717 $\endgroup$
    – Ram RS
    Aug 16, 2020 at 22:04
  • $\begingroup$ @ATpoint why is that a valid reason to close? The internet is not non-redundant $\endgroup$ Aug 17, 2020 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, 2020 at 21:18
  • 3
    $\begingroup$ 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. $\endgroup$ Aug 18, 2020 at 2:08

1 Answer 1


I would recommend a specific tool for viral meta genomics rather than using applying a general tool into a specific technical challenge. Here are the ones discussed on Bioinfo SE for de novo metagenomic assembly tested/being applied to viruses. It is not an exclusive list and needs further discussion.

SAVAGE https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411778/ Baaijens et al. De novo assembly of viral quasispecies using overlap graphs Genome Research 2017 May; 27: 835–848.

S-aligner https://www.biorxiv.org/content/biorxiv/early/2021/02/02/2021.02.02.429443.full.pdf Juanjo Bermúdez s-aligner: a greedy algorithm for non-greedy de novo genome assembly 2021 bioRχiv February: 1-7

Rey http://denovoassembler.sourceforge.net Sébastien Boisvert et al Genome Biology. 2012 13:R122, December


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