Rasmus Kirkegaard

Circular contigs in the graph file displayed with funky shapes

1

Hi First of all thanks for a very cool tool. It is very handy to visualise the assemblies and provides a great understanding of how stuff is connected. I have...

Option for pacbio CCS/HiFi reads

4

Hi Ryan Great job. Looks like yet another really cool tool solving a bunch of important problems with long reads! I noticed that you have option for pacbio reads. However,...

Wiki on experimental strategies for training models with extended alphabet

1

Hi It would be cool if there was a wiki section that would include the entire approach (including the wetlab part) of training new models. e.g. what would be the...

bonito basecaller to have a resume mode

2

Hi It would be great if the bonito basecaller had a --resume mode in case something crashes or more reads are generated to avoid having to basecall everything from scratch...

"GPU option"

2

**Is your feature request related to a problem? Please describe.** When medaka cannot locate a GPU it will keep running on CPUs. **Describe the solution you'd like** It would be...

Align model names

2

Hi Keeping track of all the ONT version numbers can be a bit tricky. Maybe it would be relevant to align the names from the guppy basecaller with medaka. Now...

drep to consider rRNA genes?

2

Hi Thanks for a great tool. Have you considered a scoring scheme taking the presence of e.g. rRNA genes into account to prioritize bins meeting more of the MiMAG requirements?...

Long read support?

6

Hi Any plans to expand snippy with support for pacbio and nanopore reads? Noticed this tutorial demonstrating the cool stuff snippy can do https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/microbial-variants/tutorial.html and came here to check it...

Models for 6mA methylations coming?

6

Hi Any plans for expanding to include models for 6mA methylations? Best regards Rasmus

Expected release of all-context methylation models for kit 12?

2

Hi Any estimate on when we can expect to get methylation models for kit 12? I have experienced a growing interest in getting bacterial genomes with methylation profiling after kit...