Alexander S Yip

Hi @serathius , I could give this a shot, but I would like to understand the proposed changes a little better. Are all 4 changes necessary to address the problem?...

Try using the command line argument --optical-distance=-1 Also, is there a reason you're setting --clib-padding=1000 ? How long are your reads?

Setting the clip-padding to 1000 should not cause wrong results, but it will cost you in computational efficiency. I'm confused to how you have 5' alignment distance of 180 when...