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2.5 years ago
Michael ▴ 270
What is your opinion on ABySS vs. MaSuRCA for Illumina only assemblies (de novo)?
- 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?
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)
This is a pretty clear answer ;) Just wondering, did you ever do Illumina only with MaSuRCA?
no, that I have to admit (hence also the "biased" in my prev post :) )