ABySS vs. MaSuRCA -- opinions
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3.5 years ago
Michael ▴ 270

What is your opinion on ABySS vs. MaSuRCA for Illumina only assemblies (de novo)?

I have:

  • Genomes about 1GB in size
  • Di- or Tetraploid
  • About 60x coverage
  • Paired-end 150bp Illumina

Would you go for ABySS or MaSuRCA? Or do you even have another one you would pick? I think ABySS should be faster. But I do not have experience with the recent versions of the two assemblers, so I can not judge the assembly qualities.

What are the reasons for your suggestion?

assembly sequencing • 750 views
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ABySS!! but I'm biased :-) , as that is the one I most often use for larger genome.

in my experience it's more efficient (resource wise, quite good parallelisation, very well suited to run on a HPC ) , it's well maintained (developers usually pick up your issues quite quickly), and there is a whole suite of related (post-processing) tools.

For the 22Gb genome I recently did, it was also one of very few that was able to process my 9Tb of input files and finish in reasonable time (and with doable memory consumption)

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This is a pretty clear answer ;) Just wondering, did you ever do Illumina only with MaSuRCA?

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no, that I have to admit (hence also the "biased" in my prev post :) )

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