Body: <p>I  am trying to assemble a plant genome using AWS resources using velvet. Plant genome is huge (> 10 times human genome) and coverage is around 30 x. We are planning for de novo assembly with Velvet (threads enabled).</p>
  
  <p>I would like to know if there is a calculator that can provide approximate time taken for assembly, given the necessary details. For eg. if I furnish RAM, CPU (type of instance), genome size, approximate coverage, type of sequencing (PE or SE) and number of client nodes, it should give me the number of hours or days that would take for assembly (reference and/or de novo).</p>
  
  <p>Note: Previously posted on biostars, but no replies. </p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-17T16:18:53.530Z
Comments.Text: I don't know much about assemblies, but do you know how complex it is? chromosomes, repeated regions and other information about the complexity of the DNA? Are you using long reads or short reads (I think that short-reads, but just to make sure). Lastly, could you provide the link to the post on biostars? (Just so if someone answers there people who find this post know where to look for)
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-17T17:08:45.747Z
Comments.Text: BioStars link: https://www.biostars.org/p/348943/
Comments.UserDisplayName: h.mon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-18T20:36:46.717Z
Comments.Text: IMO this is unknowable, which is why you received no reply on biostars.
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-19T14:24:40.597Z
Comments.Text: Velvet won't work for a 30Gb genome for sure. You might have a better chance with assemblers capable of human assembly, such as soapdenovo and discovar. But even with them, probably you won't get reasonable results.
Comments.UserDisplayName: user172818
Tags: <ngs><read-mapping><assembly>
Title: Calculating alignment/mapping time
ThreadText: # Calculating alignment/mapping time
  
  (Asked by: username_0 on 2018-11-17)
  
  I am trying to assemble a plant genome using AWS resources using velvet. Plant genome is huge (> 10 times human genome) and coverage is around 30 x. We are planning for de novo assembly with Velvet (threads enabled).
  
  I would like to know if there is a calculator that can provide approximate time taken for assembly, given the necessary details. For eg. if I furnish RAM, CPU (type of instance), genome size, approximate coverage, type of sequencing (PE or SE) and number of client nodes, it should give me the number of hours or days that would take for assembly (reference and/or de novo).
  
  Note: Previously posted on biostars, but no replies.
  
  **Tags:** ngs, read-mapping, assembly
  
  > **Comments:**
  > **username_1**: I don't know much about assemblies, but do you know how complex it is? chromosomes, repeated regions and other information about the complexity of the DNA? Are you using long reads or short reads (I think that short-reads, but just to make sure). Lastly, could you provide the link to the post on biostars? (Just so if someone answers there people who find this post know where to look for)  
  > **username_2**: BioStars link: https://www.biostars.org/p/348943/  
  > **username_3**: IMO this is unknowable, which is why you received no reply on biostars.  
  > **username_4**: Velvet won't work for a 30Gb genome for sure. You might have a better chance with assemblers capable of human assembly, such as soapdenovo and discovar. But even with them, probably you won't get reasonable results.  
  
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  ## 0 answers
  
  