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Hi GraphBin group, I was able to run GraphBin and get output that looks correct for the majority of my files. I have a subset of 8 of my 45 files that are all getting the same errors. I have double …
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It would be really cool if you could add a subcommand that simply returns the path a genome/ long read takes through the graph (as a sort of graph alignment heuristic). Is that something you can integ…
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```
% Bifrost --version 2> /dev/null
Bifrost 1.0
% echo $?
0
```
Thanks - will make conda and brew recipes more robust
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Implement a `SeqGraph` version of the junction trees described in Kiran's paper. For now we can do something naive about reads with errors corresponding to pruned edges, such as skipping the remainde…
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As part of the effort to use linked de Bruijn graphs in assembly, we should eliminate the hacks that we use to mitigate the problems with cycles. Eventually this should become the only thing we ever …
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I can't seem to see what the consensus about how to write this is.
I just want it consistent. Any suggestions? I'm leaning towards "De Bruijn graphs".
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here we will write tasks, brainstorming, discussions, questions, etc. for projects
Brando's availability
Monday 4-6pm (or even 7pm)
Thursdays 5-6:30pm
Fridays 4-5pm (or even 7pm)
weekends by …
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Thanks @GuillaumeHolley and @pmelsted for such an excellent application! I have been using it for the past couple months and it has worked very well.
I just wanted to reach out to hear your thought…
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Hi,
I've just recently discovered Bifrost and it sounds like a great tool for fast homology search as evidenced by the paper presenting BlastFrost. I'd love to start using both, however, I'm runnin…
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The *de novo* discovery routine can be multi-threaded by first loading up all GATB de Bruijn graphs (this cannot be done multi-threaded) and attaching them to their respective `CandidateRegion`. Then …