Kristoffer
Kristoffer
**Seeding** At the seeding step, the current algorithm selects, for each syncmer (start strobe), a downstream strobe from a set of downstream syncmers in a window. It is obvious that...
Firstly, thanks for creating minialign! I noticed `-f` option have a large impact on the runtime and memory. Does `-f` have the same meaning as option -f in minimap? Also,...
### Background Randstrobes is a method for linking two or more k-mers together into a seed that can be used for sequence mapping. I intend the below post to be...
Originally reported as arising from issue #2. If the length of the quality value fields differs from the length of the sequence, uLTRA will align only a subset of the...
I tested increasing `-M` (default 20) to 80, this improves accuracy a bit but reduce speed, as expected. We currently try 20 locations regardless of hamming or SSW was invoked....
It would be nice to have support for both open syncmers (current) and closed syncmers (implemented here with the same density: https://github.com/ksahlin/strobealign/commit/1aba24a5fd271ebd6b8d4db022f56a1ae9755c73). Closed syncmers have a window guarantee but less...
For logging and coming back to later: Currently, we have `randstrobe(l, u, q, max_dist, std::max(0, k / (k - s + 1) + l), k / (k - s +...
The idea of joining nearby NAMs for increased score/power and to reduce redundant alignments seem logical. However, it hasn’t worked as effectively as expected. I found one reason, that I...
Strobealign could exit early, i.e., not compute `merge_hits_into_nams_forward_and_reverse()`, if `nonrepetitive_fraction` is higher than the threshold we have since strobealign will anyway have to enter `find_nams_rescue()` The only case this would...
Hi @marcelm (CC @Itolstoganov) Currently we shuffle on chunk_ID, which makes read mappings different for different number of threads, or if reads are occurring in different chunk. IIRC, BWA-MEM gets...