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Hi Dr. Guan,
I'm running your software on a large genome with ~20% duplicated orthologs as ID'd by BUSCO. The input data are PacBio CLR reads. I am seeing minimal improvements on duplicates, can yo…
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Hi,
Thanks for developing this great software!
I have encountered an error in the polishing step when running Abruijn on a mixed/metagenomic 1D Nanopore-dataset (many organisms with varying cove…
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**Related To**
- [ ] Bactopia
- [x] Bactopia Tools
**Is this related to a problem?**
Now that we have core genome MLST (cgMLST) and whole genome MLST (wgMLST) methods out there,
it would be…
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Hi,
I've successfully installed HyDe and run both the test data, along with some test data of my own (5Kb sequences of the whole genome data below).
Now, I'm trying to input whole genome sequences…
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Hello Sir,
I hope you are doing well.
I am trying to use genome scope in order to know the percentage repeat content of the genome. I am having a hard time understanding the output. Can you plea…
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Hi Roth,
Thanks for your nice presentation last week on Pangenome analysis. I am wondering how CDHIT performs when there are a lot of genomes to compare. As you might know, uclust (embedded in usear…
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Hi @xcggates
Thanks for your beautiful code!
when I use MACS2 and Clipper to call peak, I follow the steps described in [vignettes](https://github.com/JSB-UCLA/Clipper/tree/master/vignettes)/C…
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```
What steps will reproduce the problem?
1. running orthAgogue on a large (20 Gb) blast output file
What is the expected output? What do you see instead?
the expected output is the default orthAgog…
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Hi,
Do you think your LACHESIS pipeline could be applicable to Chicago ((Cell-free Hi-C for
Assembly and Genome Organization) data?
I imagine that the data produced by the Chicago methods should loo…
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The reason multiple insert libraries are used is to strike a balance between long and short range information. Long-insert mate pair libraries are great at telling you two contigs are linked but doesn…