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BWA-mem2 vs Bowtie2: no deterministic option

Hello, I know that with Bowtie2 I can choose the --non-deterministic option to make sure that the pseudo random generator is re-initialised differently every time the algorithm runs. Would this be possible to do such thing with BWA-mem2 as well? and if yes, how does the two algorithms, the one used by Bowtie2 and the other used by BWA-mem2, compare?

bowtie2 bwa alignment
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updated by Ram Ram • written by alessandra.vittorini • alessandra.vittorini

1 answer

You can add -K 10000000 to your bwa-mem2 call, then it should run deterministic. See for instance this thread: -K

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written by DBScan • DBScan

DBScan So, it implies that if I don't use this option -K some number, it is NOT deterministic? However, I still don't understand how the random seed is selected.

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written by alessandra.vittorini • alessandra.vittorini

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