I am having single end reads from Ion Torrent. I also did my de novo assembly with Spades( SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing) , MIRA and also I am using CISa : Contig Merger (http://sb.nhri.org.tw/CISA/en/Instruction) for single end reads .
Now if i merge the contig file from both the program which program i can use for this job??
After merging the contig the quality of draft genome will increase or not ??
If any one have experience please help me out ..
Thank you advance