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Derrick,
I notice that often my pure bacterial samples still get 5% say of reads being unclassified. When I assemble these reads, they turn out to be bacterial plasmids.
The problem is that _some_ o…
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Hello,
https://flanker.readthedocs.io/en/latest/
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I am having difficulty understanding some of the information in the documentation. In order to fully understand and reproduce the information…
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How do I make/use a custom DB?
There are some input files that are not specified
% mob_cluster --mode build -f new_plasmids.fasta -p new_plasmids_mobtyper_report.txt -t new_plasmids_host_taxonom…
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Especially for allele description in papers where the plasmid is given by name but sequence can't be found, if the plasmid has only been used to clone a fragment, and then clone it out.
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`sourmash compute` is using `--name-from-first`, which might pick up the wrong name. Some bacterial genomes in genbank have plasmids, and if they are the first sequence it's going to mess up classific…
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Dear Developers,
I wanted to test metaviralspades on a sample that contains pooled RNA from thousands of plants. Previously, I used regular SPAdes for the assembly which worked quite well. Now, I r…
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View 1: strains with associated genes
View 2: strains with associated phenotypes?
Each display will show a list of these related strains with an option to swipe/click to view another set of relate…
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I am looking for a more detailed description of the binning process for Hyasp plasmids. I set the binning parameter to -b 1, which I think means that it will group plasmids together if they are one st…
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Just a suggestion for the [database build step](https://bioinf.shenwei.me/kmcp/database/#gtdb). Since the sample size is pretty big, it's worth using the [`--enable-score-calibration` in geNomad](http…
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Like we did for #1.
We are currently waiting for some preliminary data to converge and names to be nominated:
https://twitter.com/armish/status/1183753089637064707