Answers.Body: <p>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 <em>de novo</em> metagenomic assembly tested/being applied to viruses. It is not an exclusive list and needs further discussion.</p>
  <p>SAVAGE
  <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411778/" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411778/</a>
  Baaijens et al. De novo assembly of viral quasispecies using overlap graphs Genome Research 2017 May; 27: 835–848.</p>
  <p>S-aligner
  <a href="https://www.biorxiv.org/content/biorxiv/early/2021/02/02/2021.02.02.429443.full.pdf" rel="nofollow noreferrer">https://www.biorxiv.org/content/biorxiv/early/2021/02/02/2021.02.02.429443.full.pdf</a>
  Juanjo Bermúdez s-aligner: a greedy algorithm for non-greedy de novo genome assembly 2021 bioRχiv February: 1-7</p>
  <p>Rey
  <a href="http://denovoassembler.sourceforge.net" rel="nofollow noreferrer">http://denovoassembler.sourceforge.net</a>
  Sébastien Boisvert et al Genome Biology. 2012 13:R122, December</p>
  
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Body: <p>I have sequencing data of a few samples of a DNA virus.</p>
  <p>I'd like to learn <em>de novo assembly</em> of 'short read' data, to construct a scaffold and then count the abundance of each strain in the data.</p>
  <p>I heard about <code>SPAdes</code> as a good choice for these kinds of very short genomes. and also <code>BBmap</code> for statistics related to contigs.</p>
  <p>I new to <em>de novo</em> assembly could you also recommend introductory material? For example a full workflow post/paper on genome assembly.</p>
  <p>I have some experience with RNA-seq and small RNA-seq data.</p>
  <p><strong>Note</strong>: 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 <code>aligner</code>.</p>
  <p>cross-posted in <a href="https://www.biostars.org/p/455717/" rel="nofollow noreferrer">biostars</a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-16T22:04:36.777Z
Comments.Text: https://www.biostars.org/p/455717/
Comments.UserDisplayName: Ram RS
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Comments.Text: @ATpoint why is that a valid reason to close? The internet is not non-redundant
Comments.UserDisplayName: Chris_Rands
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Comments.Text: 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.
Comments.UserDisplayName: Reza Rezaei
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Comments.Text: The subject area is huge, viral meta genomics, and there are lots of discussion (from a more specific/technical base) on Bioinformatics SE.
Comments.UserDisplayName: M__
Tags: <genome><assembly><covid-19><scaffold><virus>
Title: Resources to learn genome assembly workflow for small genomes (like viruses)
ThreadText: # Resources to learn genome assembly workflow for small genomes (like viruses)
  
  (Asked by: username_0 on 2020-08-16)
  
  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](https://www.biostars.org/p/455717/)
  
  **Tags:** genome, assembly, covid-19, scaffold, virus
  
  > **Comments:**
  > **username_1**: https://www.biostars.org/p/455717/  
  > **username_2**: @ATpoint why is that a valid reason to close? The internet is not non-redundant  
  > **username_0**: 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.  
  > **username_3**: The subject area is huge, viral meta genomics, and there are lots of discussion (from a more specific/technical base) on Bioinformatics SE.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2022-03-05. Score: 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
  
  
  ---
  
  