ALLPATHS-LG libary prep question

[kmkocot]

Hi all,

I'm interested in using ALLPATHS-LG for a genome project. I've read their manual (ftp://ftp.broadinstitute.org/pub/crd...-LG_Manual.pdf) and I'm a bit confused about the libary prep requirements. I think the author and I use slightly different terminology and want to make sure I understand what kind of libraries I will need.

The manual states: "ALLPATHS-LG requires a minimum of 2 paired-end libaries -- one short and one long. The short library average separation size must be slightly less than twice the read size, such that the reads from a pair will likely overlap." OK I completely understand that but then it goes on to say: "The long insert library should be approximately 3000 bases long and can have a larger size distribution. Additional optional longer insert libraries can be used to help disambiguate larger repeat structures and may be generated at lower coverage." Later in the manual they use different terminology but I just wanted to be clear: this is referring to a mate pair library, not a normal paired-end library with a 3kb insert, right?

Thanks!
Kevin

[Ola]

Yes, that would be a mate-pair library.

Note that Broad moved from Allopaths to Discover with 2x250 bp reads for the 200 mammals project, so may be worth looking into if that fits in your budget. Also, the Chromium (10X genomics) looks promising for de novo scaffolding as it spans much longer regions than standard mate-pairs.