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4 votes
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What does it mean to over sample?

As you sequence a library you are sampling from the pool of all possible oligonucleotides found in it. This is a stochastic process, meaning that you are more likely to sequence a piece of DNA that is ...
conchoecia's user avatar
  • 3,181
3 votes
Accepted

Microbial Classification with 16S Nanopore Data

Use kraken2 with one of the 16S databases. Kraken2 has worked well for me with nanopore sequences. Pavian can be used to inspect the Kraken2 report files visually. Using uncorrected called reads has ...
gringer's user avatar
  • 14.7k
3 votes

How can I work out gram staining information from the species name?

The GOLD database can be used to retrieve a list of species names according to their Gram staining: go to the "Advanced search" page and select the either "gram-" or "gram+" under "Organism Fields" -> ...
mgalardini's user avatar
2 votes

Microbial Classification with 16S Nanopore Data

I would second the answer gringer gave recommending Kraken2. I would suggest using bracken to process the results from Kraken2 if you want to estimate species abundance (the raw Kraken2 results ...
Graeme's user avatar
  • 181
2 votes

Sophisticated algorithms in biological systems

There are many examples of biological systems doing computation, according to my understanding: Regulatory networks encode decision trees of significant complexity: wikipedia. Alan Turing did ...
Maximilian Press's user avatar
1 vote

Multiple genome assemblies of the same bacterial species

A couple of ideas: Use kraken2 to classify the reads. If you are able to convert your "repo" to kraken2 format, then the matching will be very fast and relatively accurate. Also, using bwa-...
Fabio Marroni's user avatar
1 vote

How to create Beta Diversity distance boxplot

You can use as.data.frame() or as_tibble() to convert/coerce your matrix to a data frame or a tibble respectively (Technically a ...
haci's user avatar
  • 4,202
1 vote

MaCconkey Agar colour change in non-lactose fermentors

McConkey agar is already red. It's trick is that it has two carbon sources. The bacteria that cannot use the more energetically useful lactose use the amino acids (peptone) generating ammonia which ...
Matteo Ferla's user avatar
  • 4,244
1 vote

What is a proper way for random subsampling of metagenomic data?

I am not NGS expert, I known ML. Essentially you are performing data augmentation which is essential for ML. What I question is whether a replicate of e6 from a population of e7 would really be ...
M__'s user avatar
  • 12.8k
1 vote
Accepted

Is there a resource where I can donwload E. coli assemblies grouped by their pathotypes?

If ENA archive contains such information, then you can access it programatically through the EBI api. Also you can access the NCBI database programatically through their eutils. In both cases you ...
aLbAc's user avatar
  • 196
1 vote

What does it mean to over sample?

I don't think there's anything inherently wrong with sequencing to high depth (though naive approaches to dealing with sequencing errors such as singleton removal may fail if the depth is so high that ...
heathobrien's user avatar
  • 1,816
1 vote

How can I work out gram staining information from the species name?

AMR R package can assign gram staining based on taxonomy. See mo_gramstain(x, language = get_AMR_locale(), ...).
fconstancias's user avatar

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