Hi! I installed this program to fill the gaps in my assembly by local reassembly but reading the usage, I don't know where should I put the reads that I want to use to help fill the gaps.

image.pl -scaffolds scaffolds.fa -prefix 76bp -iteration 1 -all_iteration 10 -dir_prefix ite

Here all the options:

> Compulsory parameters:        

> -454 (for newbler assembly)
> -velvet (for velvet assembly)
> -prefix 2540_5    (Illumina prefix lane)
> -iteration 1      (current iteration)
> -all_iteration 5  (number of iterations to be run after 1 iteration)
> -dir_prefix ite   (prefix for the iterations)

> optional parameters: 

> -kmer 31      (kmer option in velvet)
> -toignore 10      (exclude extension of less than n bases)
> -overhang 50      (to not extend if overhang has > 50bp) 
> -vel_ins_len 500  (insert length specified in velvet)
> -smalt_minScore 0       (used for -m option in smalt)

Does anyone have experience with this tool? or can recommend me another tool to fill the gaps in the assembly with more paired-end reads?

Thanks a lot for your help in advance :)