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choosing appropriate aligner #14

Open thomasfaraut opened 1 year ago

thomasfaraut commented 1 year ago

Dear LRcaller team,

I am calling SV genotypes on a dataset of 20 individuals sequenced with ONT (~40X). I am runing LRcaller in parallel on each chromosome.

LRcaller help indicates that 3 different aligners can be used : bwa, minimap2 or seqan. Using seqan, works perfectly, but requires a substantial amount of computing time. Would one of the other aligner be a solution if I am facing a computing time issue ?

Thank you in advance for your help.

Regards, Thomas

bjarnivh commented 1 year ago

The bwa and minimap options have been depricated, we will make sure to update the documentation. These aligners do not guarentee to return the optimal result. Running LRcaller might take ~1 CPU hr per chromosome per sample, it should parallize almost perfectly so should take less time with fewer cores. If this is still too slow you might change the default setting on the -w parameter, from 500 to 100 or 200.