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 :)