I am working on my first 10x Genomics de novo assembly. For those who may not be familiar with it, 10x adds barcodes to Illumina short reads coming from the same long fragments that are then used to reconstruct long "linked" reads. Since these are non-standard "linked" reads and the technology is fairly new, I don't think there are any tools available for processing the data other than the official Supernova software. Has anyone had luck with alternate assemblers for 10x data?
The reason I am asking is because Supernova is essentially failing for me. I used one HiSeq lane of input, which is fairly reasonable. Based on my discussions with 10x, that amount of data should take about a week to process. I had it going for 4 weeks and it did not finish. Then, the server had to be restarted, so the job was killed. Even half a lane did not finish after several weeks. If I use a small subset of data (like 10M or 100M reads), the process finishes. The results are terrible, but at least it shows there aren't any problems with the dependencies or the environment. I was wondering if anyone here had run into any similar problems and if they had any solutions. Normally, if a certain tool has issues, you can try a different one, but that does not seem to be the case here.