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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.

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  • $\begingroup$ 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) $\endgroup$
    – llrs
    Commented Nov 17, 2018 at 16:18
  • $\begingroup$ BioStars link: biostars.org/p/348943 $\endgroup$
    – h.mon
    Commented Nov 17, 2018 at 17:08
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    $\begingroup$ IMO this is unknowable, which is why you received no reply on biostars. $\endgroup$
    – Devon Ryan
    Commented Nov 18, 2018 at 20:36
  • $\begingroup$ 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. $\endgroup$
    – user172818
    Commented Nov 19, 2018 at 14:24

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