Robert Vaser

Hi Xinwen, racon does not stitch contigs together, it polishes each of them separately. By breaks you mean what exactly? Best regards, Robert

Hi Xinwen, racon by default does not output unpolished sequences. You can disable that with the following option -u, --include-unpolished output unpolished target sequences You can determine which of the...

Hi John, you can try with option `-f` which will enable multiple mappings per read (vs one by default) and hopefully increase the coverage at contig ends. Not sure why...

Racon uses a heuristic postprocesing method which truncates the obtained window consensus at its ends depending on the window coverage. Lets say the average coverage of a window is 50,...

Are the numbers in the table total telomere size of both ends or just one of them? Can you see if the beginning is more trimmed than the end? The...

@johnomics, the beginning of the first window and the end of the last window are not trimmed anymore on branch `feature_no_trim`. Checkout to it, compile and run like default racon...

I have also added an option to disable trimming completely (option `--no-trim`) to the same branch as above.

The problem with poa consensus is that long insertions from beginning and end of the POA graph are added into the consensus due to the heaviest path algorithm. That is...

Hi @cgjosephlee and @johnomics, using option `-c` with Minimap2 will put the CIGAR into PAF which will not be taken into account in Racon and Racon will use Edlib instead...

@cgjosephlee, Racon version `1.4.5` should be able to handle any CIGAR length in PAF so you do not have to remove them manually.