An assembly of reads, contigs and scaffolds

A blog on all things newbler and beyond

Archive for July, 2010

Running newbler: more de novo assembly parameters (and a hidden one)

Posted by lexnederbragt on July 16, 2010

Trimming (reads) by running newbler

There is a long list of options/flags/parameters for a newbler assembly, some of which have been treated in the previous post. In this post I will describe some more parameters. At the end, as a bonus, I will share a parameter that is not mentioned in the current documentation…

-ss -sl -sc -ais -ads
These parameters control read overlap detection (there are two more, -mi and -ml, which I described in the previous post). More on seeds and overlap detection is described in the post explaining how newbler works. I never change these parameters as I assume 454 has done a good job optimizing them. But I would love to hear from people that have tried the effect of adjusting these parameters… Read the rest of this entry »

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