I am very new to genome assembly. I have got 4 data for a genome of size 50M. Data what i have are, illumina short insert lib (200-500), long insert lib (300-600), mate pair (3-5kb) and nanopore (yet to receive). Kindly suggest which assemblers to use?? which data to use what stage (assembly, scaffolding or gapclosure)?? how do i get best kmer apart from kmergenie? Any other kmer identifier?
Detailed input is much appreciated.
Right now i am thinking of spades and idba_ud for assembly using both short and long insert together. Further need some assistance.