Robert Vaser
Robert Vaser
Hmmm, not sure why that would happen. Did you try raising an issue at Unicycler repository? You can also try building and running racon_test to see if racon works properly...
Hi Chengcheng, what is the coverage of your dataset? You used a reference for variation calling or the Illumina reads? Best regards, Robert
Can you please check what is the average quality of the ont reads?
There is a tiny chance that this is the issue as Racon employs a quality threshold of 10 on each windows. Try running one iteration with parameter `-q 8` and...
The fasta file will not be a problem as Racon does not use qualities in this case. I am not sure why there is a minimal difference in variations. The...
Does smartdenovo employ any accuracy boosting during assembly or is the final error equal to the error in raw reads?
Well then I think it is not that surprising that the accuracy changed a little. Maybe you can change different alignment parameters, like 2/-5/-2 or 3/-5/-4. You can also try...
Hi Devon, unfortunately I have only a single thread parser which is kinda problematic when you want to read really big files. What sizes of files are you dealing with?...
Probably the slowest part is `.paf` parsing. You can drastically reduce its size if you replace read names in your `.fq` file with integers and then rerun minimap or whatever...
I had planned to integrate timestamps in several projects but did not have the time yet. Have to decrease the number of log messages as well! :)