This post is about how to start up newbler for de novo assembly projects. I will describe setting up newbler using the command line. Most of the options I will mention are also available through the GUI version, but I will not describe how to use them here.
For a description of the progress that newbler reports during assembly, please check this post. For a description of the different output files, these are described in a series of previous posts.
1) default newbler on one or more files
This is the most simple way of running newbler: just provide it with one sff file. It will generate a folder called along the lines of P_yyyy_mm_dd_hh_min_sec_runAssembly and put all output in there. If you want to have control over the name of this folder, use
runAssembly -o project1 /data/sff/EYV886410.sff
-o describes the name of the folder newbler will provide all output in, in this case ‘project1’