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Dear Developer,
I am trying to use NanoCaller on a high coverage (2000x on Microbial genomes) datasets. When I omit the sub-sampling process, the result genotypes all turned to G
##fileformat=VC…
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I tried deeplasmid on a 100-cpu core node. I used the provided Docker image (billandreo/deeplasmid), and followed your instructions using the command feature_DL_plasmid_predict.sh. I tested on 5 diffe…
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Hi Zhichao,
I got 55 MAGs from the 6 metagenome samples, but some typical genes for some MAGs were lost maybe during the binning or refinement process. So, is it okay that I use the assembled conti…
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Hello,
I'm having some issues with BWA running on one the prebuilt databases and the error message is not particularly helpful.
Any idea what's going wrong?
```
$ /home/dcd3001/bin/gottcha -…
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This came up on microbial bioinformatics slack, thought I'd share - topic was selecting from many viral genomes.
> it should be possible to use large-scale ANI-style analyses to select the closest …
ctb updated
11 months ago
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- Keightly 2005:
- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240079/
- intro explains some of the problems associated with identifying conserved noncoding elements (CNEs)
- Siepel 2005:
- htt…
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not sure this is the right place to ask, but: is there a ball park estimate of how many reads/ bases are at least required to reliably identify an isolate of some bacterium? in terms of coverage, 1x s…
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Hi,
I am trying to download the microbial genome using repophlan_get_microbes.py script on iMac. But it is running from last 2 days and still keep running, could you please suggest how many total s…
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I was working with a sample made of 50% universal human reference and 50% a bacterial community reference. I used Bracken to get community composition and it removed millions of human reads and reall…
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Identify all (meta)genomic datasets that meet certain environmental measurement thresholds (e.g. all samples at X°C, with Y nitrate concentration, Z phosphate concentration)