Coverage and jumping libraries in ABySS

[VNou]

Hello, i am running ABySS with a fragment library of Staphylococcus aureus that i found in this site: http://gage.cbcb.umd.edu/data/index.html.
I am running abyss-pe with the following parameters:
c=50 k=45 j=16 n=10 in='frag_1.fastq frag_2.fastq' , where frag_1 and frag_2 contain the fragment libraries of the site. Every time i use a different coverage (40,50,60,100). The site that i post contains also jumping library. Should i incorporate and if yes how. Will the running without the jumping libraries result in not good outputs, and also the manner i run it is it good to have decent results? I am new in this field so i want to ask to make sure that i am not doing all the things wrong. Thank you a lot.