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
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
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