An assembly of reads, contigs and scaffolds

A blog on all things newbler and beyond

Archive for June, 2010

Running newbler: de novo assembly

Posted by lexnederbragt on June 10, 2010

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

runAssembly /data/sff/EYV886410.sff

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’

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