ALLPATHS-LG short Jump insert size

[Raff]

Hello All,

I am trying to figure out if ALLPATHS requires a 3kbp short jump insert size or if something larger like a 5 or 6kbp could be used in lieu of the 3kbp library.

The manual implies 3-10kbp will work but then I have read conflicting papers that indicate 3kbp is required but additional, larger, libraries can be added to increase power.

Maybe there is a drop off in assembly quality if you don't include a 3kbp library?

Thanks.

[ChrisAU]

Hi Raff,

I performed ALLPATHS-LG assemblies with only a 2kb or 4kb mate-pair library (additional to the paired-end library of course) without any problem or obvious drop in the assembly quality.

Chris

[Raff]

Thanks Chris,

I did contact the author of the original paper and he said the biggest worry might be difficulty in achieving high enough library complexity. However, other than that he seemed ok with the notion. Thanks for the input.