Robert Vaser
Robert Vaser
Ping @kassammo.
Hello, how long has it been stuck on this window? Maybe the window has really high coverage (due to repeats) or an infinite loop is somewhere (less likely as 7...
You can try adding `if (i != 360378) continue;` before https://github.com/isovic/racon/blob/404122e93a0716c2a2dac9493a86986a2f700be0/src/polisher.cpp#L459 Recompile and run racon again. If it still does not finish, then there might be a problem in the...
@dikkeaap, I managed to encounter the bug you mentioned on a large genome with high Illumina coverage. A window (of length 500) contained 500k reads with average quality of 50...
Hi Charlotte, can you please paste the whole Racon command? Which version of Racon did you install (you can get it with `racon --version`)? I am not much familiar with...
Hello, can you please paste the minimap2 command which generated the overlaps.paf file? Best regards, Robert
If you want to polish the assembly with reads, you need to run it like this: ``` minimap2 -a assembly-contigs.fasta (hifiasm file) raw.fastq (pacbioraeds) -o output.sam ``` Also, Racon does...
Hello Raymond, racon expects **one** file with any kind of reads (3rd gen or 2nd gen paired/single ends). Therefore, you should join your paired ends into one file but be...
Hello, you can try minimap2 with `-x sr` option. By raw miniasm assembly you used PacBio/ONT reads right? If so, I would advise polishing with those reads first (if you...
The initially polished assembly should be alright. Best regards, Robert