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Hi, I have a question regarding the --enable-score-calibration flag. I understand that it considers the composition of the sample to output a 'real' probability, e.g. plasmid score of 0.4 would mean t…
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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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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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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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Hi Seeman,
I downloaded few plasmids sequences in Genbank full format from NCBI for plasmid annotation and ran the following command:
`prokka ENT2_Contig6_len_41186_circ_NDM-1_Plasmid.fasta --ou…
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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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For plasmid you will not get a good result if you just use the default settings.
I would recommend getting GENBANK files (.gbk or .gb) of all the plasmids that are similar to your one.
Say you g…