Q1: What is systemfile...?
Ans: They are intermediate files that could be removed after execution. If the intermediate files are reserved, Clover could run faster from the intermediate result when rerun on the same inputs and the same values of parameters -k and -p.
With the function, we can rerun faster when trying other parameters.

Q2: What is -p?
Ans: it is editing distance when clustering k-mers. Clustering k-mers is our newly design method to retrieve error-robustness assembler.

Q3: How to use Clover If we don't know the insert sizes of libraries?
Ans: If we don't know the insert sizes of libraries, we could omit the parameter -is, Clover would automatic estimate the insert size.
For example, if two libraries of paired read files with unknown insert size are used: frag1.fq, frag2.fq, short1.fq and short2.fq.
Just type:
   $ clover -k 40 -p 1 -i1 frag1.fq,short1.fq -i2 frag2.fq,short2.fq






Clover: a clustering-oriented de novo assembler for Illumina sequences
Contact: jmfhsieh@gmail.com