Category Archives: Marvel assembly

Moving to Marvel

Well, Canu seems to do a reasonable job of assembling long reads for larger organisms but it is laboriously slow!! Trimming and Unitigging stages can take several weeks each. I am now using the reduced list of reads (after mapping to the mitochondrial genome – which reduced reads by ~4%) with the Marvel assembler.

https://github.com/schloi/MARVEL

I have been working through the scripts as per the Schmidtea mediterranea example from this recent Nature publication by Grohme et al 2018.

https://www.nature.com/articles/nature25473

So far so good. However the claim that by using repeat soft masking will reduce computational time by an order of magnitude is yet to be determined. Fingers crossed.