The latest version of newbler, version 2.6, has some welcome additions for input and output. As I have so far only treated de novo assembly, I will skip the updates on the gsMapper (except for mentioning that it is now able to provide a bam file using the -bam option).
Archive for the ‘Using newbler’ Category
Posted by lexnederbragt on July 12, 2011
Posted by lexnederbragt on July 16, 2010
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 »