Harish
Harish
Hi, Thank you for getting back so soon. I apologize for not being so clear in the original question. Regarding the question from the above plot, I hope that I've...
FWIW, I've taken to either blasting/aligning the reads to reference organelle genomes, fetch and subsample those out to generate the assembly. Depending on the Long-reads type and preparation, I've gotten...
@Kinggerm Does get organelle pull in Pigz as well when installing via conda? If so, that would be a lot better as pigz is foolishly fast!
Apologies to necro this thread, but would something like this help? I'm using R to generate the Biotype plot, but I've generally observed that for Ensembl annotated Animal genomes they...
@gringer Any such plots or outcomes from Bonito basecalled datasets?
Any such luck for Proteomes downloaded from uniprot?
This might be a bit tardy solution, but @MichelMoser @morispi probably an easy way out might be to gzip the paf file and uncompress+stream it for the next step?
Sorry, if I wasn't being too specific, I mean PacBio's subread BAMs, as I understand them, they are unaligned bams with PacBio Instrumentation specific metadata embedded in these bams.
You can always remove the *hd5 files if your contig assemblies have finished ;) Ofcourse I'm assuming this since you have reached the mapping stage. I also tend to remove...
@xiekunwhy Like @rchikhi said, the easiest way is to assemble the genome would to develop the contigs independently and scaffold using the Pairing and the Mate information. What type of...