How are paired ends handled?

[han...@gmail.com]

Thank you very much for the very interesting paper and wonderful results! I plan to adopt this tool in my study.

I do have a question though: after reading the paper, it still remains unclear to me as how the paired ends are handled. Please correct me if I am wrong: from the description of the Quaternary sequence tree (e.g., Fig. 1), it seems the paired ends are used independently as if they are unrelated reads from single end sequencing. Since I have a special data set which has 3 sequencing data from a single subject but with different insert sizes, so I would like to make use of the known isize information. Are there some parameters that I can optimize for my special case?

I tried to dig into the source code to get some idea on this matter; however, it appears that all the algorithm parts are hidden in the precompiled getway_s or asm. So it would be great if you can point me to the source codes for getway_s and asm (even outdated versions should be fine).

Many thanks,
qazhus

[SMufin]

Hello Qazhus,

SMuFin do not use paired end information. So, currently, out method cannot take advantage of library size information.

Regards,