I have done Bacterial genome sequencing using Illumina Hiseq PE *150b , my library contains 600k reads, But after assembling with spades ( Kmer = -k 21,33,55,77,99,111,127) the result is too bad. I have got ~3400 contigs. I have no ref. genome for my bacteria now, we only know its family. My GC content = ~70%
What is your suggestion for decreasing number of contigs? Is there any other options better than Spades for bacteria genome assembly?