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The current CoL uses a higher classification that evolved over time and is in many groups defined by the respective GSD. This causes for example all algae classes and even phyla to disappear when Alga…
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Hello,
I am a new user to phyloseq and have a quick question with regards to data display. I know that there is the function sample_sums(x) which returns the number of sequences per sample, but I am …
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The current CoL uses a fixed set of ranks that limits its use and misses some important groups.
It is suggested to extend the ranks to cover the following, bold=existing CoL ranks:
**kingdom**
**…
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Hi,
I keep getting the following error when i run SqueezeMeta on a minion metagenomic sample.
`Running jobs. First attempt out of 2.
Starting 'obtovl' concurrent execution on Wed Mar 18 14:25:…
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Hi Derrick,
I tried classifying my sample reads with kraken database containing only "nt" sequences and found that all my reads were classified at the root. Here is the output from the first few li…
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Teresa to ask Phyllis
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Dear all,
I have managed to successfully run GTDBTk on my "high-quality" genomic bins as defined by CheckM, but am having some issues interpreting the results. I have attached the output file.
I…
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Hi,
The CLI of `ganon classify` indicates it will report results at species+. I took this to mean subspecies/strains as defined by the NCBI Taxonomy. However, I have yet to observe classifications …
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It's come to our attention that the V6-V8 custom taxonomic classifier (re-generated on Aug. 20th 2019) can result in incorrect assignments (by setting almost all ASVs to the genus _Alteromonas_ for ce…