Robert Vaser
Robert Vaser
Hello, do files `PA_hifi.fa` and `minia_contigs_Pseudomonas.contigs.fa` have a sequence with the same name but different data? Racon has error correction mode for which we included a check that if a...
Hi Niccolo, you have to reorder HiFi and CLR reads in your pbmm2 command (first CLR reads which are the "reference" on which you map the HiFi reads). As you...
Hi Lingyun, I have not evaluated HiFi vs Illumina polishing so far, so I cannot advise you. You could first polish with HiFi, and afterwards with Illumina, and evaluate the...
Hello, please paste the command you run to get the mapped.sam file. Best regards, Robert
Please run `head -n1 ILPE_unclassified_1.fastq` and the same for `ILPE_unclassified_2.fastq`.
Please rerun bwa-mem with the combined file ILPE_joined.fastq. The problem is that reads after the preprocessing script have different names in .fastq and in your .sam file, and Racon will...
Hello, Racon loads all the input files into memory, hence the high memory consumption. You could try using the racon_wrapper to downsample the reads, but that might affect accuracy. Best...
Hello, sorry for the late response! Unfortunately, Racon only accepts SAM as alignment input. We will add BAM support in the new release. Best regards, Robert
Hi Cedric, unfortunately no BAM support was added yet. Best regards, Robert
Piping was removed since version `1.0.0`.