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NTR: microbiome sequencing design
definition: The microbiome comprises all of the genetic material within a microbiota (the entire collection of microorganisms in a specific niche, such as the human …
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Hi, I have a question about the import_biom function. When I import my biom file, if I extract as data frames the sample data, the otu table and the taxa table, the first column is the index of the da…
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E.g.
```
/ NCBITaxon:1 ! root
is_a NCBITaxon:12908 ! unclassified sequences
is_a NCBITaxon:408169 ! metagenomes ***
is_a NCBITaxon:1235509 ! synthetic metagenome
is_a NCBITaxon:256318 ! …
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MIxS and MGnify both provide controlled hierarchical vocabulary for different kinds of environments. For our purposes it is essential to distinguish between biotic vs. abiotic environment as the top l…
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This should be done as a pre-processing step, part of overall ETL pipeline, such that each individual analysis does not need to do normalization
Currently done for water packages here:
https://nbv…
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Hi, sean! Recently, I read your article 'Thousands of previously unknown phages discovered in whole-community human gut metagenomes'. And I am very curious about the phylogeny method in the article an…
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I am very interested in the development of strainberry, especially as it applies to metagenomics with PacBio HiFi data. I wanted to draw your attention to a new PacBio dataset I recently uploaded to N…
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seeing if a sample is in the database / identifying if sample is there
differential privacy/dbgap search (at level of technical replicates)
biogeography - where might I look
discovering more …
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The accession BK010471 is for a crAssphage that is ubiquitous in human gut metagenomes ([link](https://www.nature.com/articles/ncomms5498)), and in particular is found in the 454 data set SRR073439.
…
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Dear developers,
I would like to use HumGut and Kraken2 to analyze some human gut microbiome data, and expanding the database to include other taxonomical groups not covered by HumGut, such as Prot…