Johannes Debler

@zacksaud no worries. It's not ideal, but it solves the problem you have. Preferably something similar will get rolled into funannotate in the future including maybe batter EC allocation, as...

Yes, the same version installed via mamba/conda works fine: Conda version:  Docker version:  Any chance you can try to replicate this via docker to rule out any problems...

Same problem here. Just installed via conda and keep running into this error when providing alignments in bam format.

I think I got it, using a combination of kpRect and kpPoints :-)

Thanks for that. I've used kpRect, I'll check out kpSegments. The scale bar would be nice, but in the short term I'll just add it in Inkscape :-) Would be...

Thanks. Where can I find the NextDenovo corrected reads? I couldn't spot them in the output directory.

Thanks, found them. And yes, telomeres are missing from those corrected reads.

@webbchen I did not. My workaround is that I assemble with both Flye and NextDenovo. ND seems better at assembling big repeat rich regions which Flye breaks into separate contigs....

Actually, you can ignore the linux base update in this Dockerfile, it is only necessary in the nf-repeatmasking file where genometools are installed. This one builds fine, so only update...

You can extract them, it's just a bit annoying as it basically means basecalling twice. At least that's what we are currently doing. Basecall in simplex mode, classify into barcodes,...