replacing nucmer
Closing the gaps in scaffolds with preassembled contigs
Brought to you by:
s-kosugi
Menu
▾
▴
#4 replacing nucmer
Have you considered swapping out mummer for something faster, say E-MEM?
https://github.com/lucian-ilie/E-MEM
We'd like to replace our current gap closing tool but we process a lot of fungal genomes, some of which can be quite large so are looking for something faster than nucmer.
Thank you for providing the useful comment.
I would consider to use E-MEM as a replacement of MUMMER/Nucmer in the future.
Currently GMcloser can use blastn in place of Nucmer by using the option -b.