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This is an incomplete list, but for example:
1. "too many open files" errors occur in Bash for large numbers of genomes. At a minimum adjusting ulimit for these might be a good idea, but it would b…
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Will need this to highlight in the eventual publication
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Hi Diener,
would it possible to provide detailed description on the procedures that generated those GEM reference database? I found it quite useful while I am hesitating to use it in my manuscript wi…
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- [ ] Editor should be able to handle giant sequence loaded
- [ ] onSave hook should have option to just save the changes
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Hello @cdanielmachado, other developers and all in the community,
I am interested in performing analysis on my genome-scale community model, which I created using CarveMe. Specifically, I want to u…
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We have two options here: cluster style allreduce or hogwild, we need back of the envelope calculations for which of the two is best. Assuming current machine is on a spinning disk, figure out howmuch…
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I'm working on scaffolding a HiCanu assembly for a shark species that has had duplicates purged. It was assembled with ~45x PacBio Hifi (Median length: 13,710 bp; Mean length: 13,590 bp; Max. length: …
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title: OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes
DOI: 10.1073/pnas.1714530115
url: https://pubmed.ncbi.nlm.nih.gov…
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## Report files from updating genbank databases
https://farm.cse.ucdavis.edu/~baumlerc/report.20240712-archaea.html
https://farm.cse.ucdavis.edu/~baumlerc/report.20240712-fungi.html
https://farm.…
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I'm trying to sketch the [RVDB, the Reference Viral Genome Database](https://rvdb.dbi.udel.edu/). The clustered file is ~600 MB.
```
sourmash scripts manysketch C-RVDBvCurrent.manysketch.csv -o C-…