I use Newbler to assembly chloroplast genome, with 2 fastq files. It's almost 1.2 million pair reads.
I run the program in my computer(Core i7, 16G RAM) since the day before yesterday.
From yesterday to this morning, the log files shows the same: Computing alignment, 1209000. And all reads are 1212000.
Please tell me how to set the parameters or do somethings else. I don't want to wait several days.