Answers.Body: <p>I've been using <a href="http://kmer.sourceforge.net/wiki/index.php/Getting_Started_with_ATAC" rel="nofollow noreferrer">ATAC</a> to successfully align different versions of the rice genome assembly. There is a chance it will work for you between two closely related species (potato and tomato work well for example).</p>
  
  <p>It's not massively user friendly, but it's very fast, and it produces long, 'clean' alignments (i.e. almost all 1 to 1 alignments). The output format is a bit cryptic (zero-based start position and length instead of the more usual 1-based start and end positions), but as I said, it should basically output the order for you in about 30 minutes.</p>
  
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Answers.Text: That looks like a good solutions. I hopt this will help me to align scafolds
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Answers.Body: <p>Have you tried <a href="http://darlinglab.org/mauve/mauve.html" rel="noreferrer">Mauve</a> alignment? Its pretty easy once you become familiar and has a GUI for further ease of use. Additionally there are a few online tutorials on how to re-order contigs/ scaffolds using this software. Heres <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723005/" rel="noreferrer">one I use</a> when in need.</p>
  
  <p>Mauve contains a function called <a href="http://darlinglab.org/mauve/user-guide/reordering.html" rel="noreferrer">Mauve Contig Mover (MCM)</a> which can be used to a) compare an assembly to a reference and/or b) rearrange contigs to improve assembly quality.   </p>
  
  <p>I use the tutorial as above which uses the GUI for Mauve. I</p>
  
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Answers.Text: Could you please expand this and give an example of how Mauve can be used for the OP's purposes?
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Body: <p>I am trying to reorder scaffolds of a rice species, but no genetic map is available right now. <em>Oryza sativa Japonica</em> is a close relative of this rice species. Mummer was used to do a whole genome alignment, and I am trying to reorder scaffolds according the mummer result. But I found it's too complicated to do this by myself, many scaffolds may align to multiple Oryza sativa Japonica chromosomes or multiple loci in the same chromosome.  </p>
  
  <p>What software can I use to handle this task?</p>
  
Tags: <phylogenetics><assembly><software-recommendation><scaffold>
Title: Reordering scaffolds according to a reference without a genetic map
ThreadText: # Reordering scaffolds according to a reference without a genetic map
  
  (Asked by: username_0 on 2017-07-11)
  
  I am trying to reorder scaffolds of a rice species, but no genetic map is available right now. *Oryza sativa Japonica* is a close relative of this rice species. Mummer was used to do a whole genome alignment, and I am trying to reorder scaffolds according the mummer result. But I found it's too complicated to do this by myself, many scaffolds may align to multiple Oryza sativa Japonica chromosomes or multiple loci in the same chromosome.
  
  What software can I use to handle this task?
  
  **Tags:** phylogenetics, assembly, software-recommendation, scaffold
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2017-07-11. Score: 2 | Accepted answer
  
  I've been using [ATAC](http://kmer.sourceforge.net/wiki/index.php/Getting_Started_with_ATAC) to successfully align different versions of the rice genome assembly. There is a chance it will work for you between two closely related species (potato and tomato work well for example).
  
  It's not massively user friendly, but it's very fast, and it produces long, 'clean' alignments (i.e. almost all 1 to 1 alignments). The output format is a bit cryptic (zero-based start position and length instead of the more usual 1-based start and end positions), but as I said, it should basically output the order for you in about 30 minutes.
  
  > **Comments:**
  > **username_0**: That looks like a good solutions. I hopt this will help me to align scafolds  
  
  ---
  
  ### Answer by username_2 on 2017-07-11. Score: 5
  
  Have you tried [Mauve](http://darlinglab.org/mauve/mauve.html) alignment? Its pretty easy once you become familiar and has a GUI for further ease of use. Additionally there are a few online tutorials on how to re-order contigs/ scaffolds using this software. Heres [one I use](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723005/) when in need.
  
  Mauve contains a function called [Mauve Contig Mover (MCM)](http://darlinglab.org/mauve/user-guide/reordering.html) which can be used to a) compare an assembly to a reference and/or b) rearrange contigs to improve assembly quality.
  
  I use the tutorial as above which uses the GUI for Mauve. I
  
  > **Comments:**
  > **username_3**: Could you please expand this and give an example of how Mauve can be used for the OP's purposes?  
  
  ---
  
  