is there a chromosome length limit?

ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs

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is there a chromosome length limit? #1312

Closed eead-csic-compbio closed 6 months ago

eead-csic-compbio commented 6 months ago

Hi, does minigraph-cactus support chromosomes of any length or is there a limit instead? Thanks

glennhickey commented 6 months ago

If you're chromosomes are under 2 gigabses I think it should work okay. After that I'm not sure. What size is your input?

eead-csic-compbio commented 6 months ago

All chrs are smaller than that, so it should be fine : chr1H_LR890096.1 516505932 18 80 81 chr2H_LR890097.1 665585731 522962293 80 81 chr3H_LR890098.1 621516506 1196867864 80 81 chr4H_LR890099.1 610333535 1826153345 80 81 chr5H_LR890100.1 588218686 2444116068 80 81 chr6H_LR890101.1 561794515 3039687506 80 81 chr7H_LR890102.1 632540561 3608504471 80 81 I was asking because we had to split them in two to be carry out GATK analyses, thanks!