abyss/konnector2 : Usage Scenario
Sven
I'd just like to point to my https://www.biostars.org/p/163717/.
Quite a few views but currently no answer. Maybe someone here can answer my questions?
thanks,
Sven
Ben Vandervalk
Hi Sven,
Good questions.
Regarding your first question about long run times with Konnector2:
* It is important that the Bloom filter FPR stays below 25%, or the graph search algorithm may run forever. FPR decreases linearly when increasing the Bloom filter size and FPR increases linearly with the number of distinct k-mers in your data set. Sorry, there is no easy way to choose the right Bloom filter size other than learning about Bloom filters and understanding the math (the Konnector2 Bloom filters use a single hash function). But as a quick guideline, I recall needing about 40GB for an 80X human dataset.
* Konnector has a known issue where it will sometimes stall at low k values (typically values in the range of k=20..60). Unfortunately there is no fix for this at the moment, but it is something to be aware of. Run konnector with the verbose flag (i.e. "-v") and you will be able see regular progress messages to verify that your jobs are proceeding successfully.
Regarding your second question, I recommend the following configuration:
se = merged/extended konnector2 reads + unmerged/unextended konnector2 reads
pe = raw PET
mp = raw MPET
--
You received this message because you are subscribed to the Google Groups "ABySS" group.
To unsubscribe from this group and stop receiving emails from it, send an email to abyss-users...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.