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ksahlin / strobealign

Aligns short reads using dynamic seed size with strobemers
MIT License
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Guidlines for all alignments / high sensitivity #252

Closed kcleal closed 1 year ago

kcleal commented 1 year ago

Hi @ksahlin, Thanks for the great tool. What would be your recommendations for generating as many alignments as possible for a given read. bwa has an -a option for outputting all alignments - these will end up as a bunch of secondary alignments in the output along with a primary alignment. I was trying to find a similar option in strobealign. I can see options such as -f [FLOAT] Top fraction of repetitive strobemers to filter out from sampling and -M [INT] Maximum number of mapping sites to try.

marcelm commented 1 year ago

You can use -N to get secondary alignments:

      -N [INT]      Retain at most INT secondary alignments (is upper bounded by -M and
                    depends on -S) [0]

Note that we currently still have an off-by-one error so that you would need to provide -N 2 to get up to one secondary alignment, but if you use it with a high number anyway, it doesn’t matter.

kcleal commented 1 year ago

Thanks @marcelm, I will give it a try