Robert Vaser
Robert Vaser
I am not familiar with SLURM, but Devon managed to run his script by adding `#SBATCH --error=racon.log` and `#SBATCH --output=contigs.fasta`. Take a look at #86. Although, I am not sure...
Hello, could you please verify if your paired end reads have equal names up to the first white space? Best regards, Robert
Well that is probably the problem. Racon expects that all reads have unique identifiers. In your case, only half of your Illumina reads will be used in polishing. You should...
Yes, you will have to run single-end mode. Not sure if you will lose much accuracy in comparison to paired-end mode.
Hmm, quite odd that it decreases the accuracy. Would you mind sharing the data so I can investigate locally what is happening? Did you maybe try any other polisher in...
Thanks, will check it out!
I have run your data with both Racon and Pilon, and evaluated the results with dnadiff (from the mummer package). The assembly is quite fragmented, but I am not sure...
I have updated the table above with BUSCO scores (found with saccharomyceta_odb9). It seems that the breakpoints do not have that much of an impact I guess, not sure though.
Shorter assemblies after polishing are not that uncommon. Although, I am not sure why the BUSCO scores would drop. Did you try Pilon in the same setting?
No idea why. Nothing special changed between `1.3.2` and `1.3.3`. If you had PE reads, did you combine them as described above?