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In running a CONSTAX job on the MSU HPCC there were some strange results in taxonomy assignment. For details I do have to give that I suspect may be relevant, I had the job train using the UNITE gener…
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I have figured out how to export relative abundance tables according to their taxonomic rank, but am struggling with several "unclassified" which I would prefer to be able to classify at the next high…
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Hello there!
I'm creating some Jupyter Notebooks for MGnify team to show examples of how to use the tool and I learned that the tool is filtering out samples during the phyloseq object building step.…
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### Description of feature
I can add a module to Amliseq that would run the LCA scripts from eDNAFlow. More information can be found here: https://github.com/mahsa-mousavi/eDNAFlow#lca-lowest-common-…
a4000 updated
11 months ago
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We should create exports of the taxonomic assignments for all Rfam families. This is basically what is done the rfam-taxonomy repo but the exports should be part of our FTP. I'm thinking we should use…
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Hi,
I'm building a custom DB from a large set of genome files. I'm indicating the TaxonId of each sequence using the `NCBI-style accession2taxid tab-separated files`. When I build the DB, it appear…
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> Taxonomic assignment is the core of targeted metagenomics approaches that aims to assign sequencing reads to their corresponding taxonomy. Sequence similarity searching and machine learning (ML) are…
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Some / many of our curiosities with MBD data could be related to non target species in data
see https://github.com/laurahspencer/DuMOAR/issues/26#issuecomment-1613501939
I think it is worth wh…
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I'm comparing MMSeqs2 taxonomic assignment with approx. 2bLCA and top hit and noticed that the later approach classifies more genes than the former. I extracted the alignments using `--extract-lines 1…
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Hi,
I came across this reading the Lin et al preprint and it sounds very useful! I have metabarcoding data for two marker (COI and 16S) from a very diverse community (I know that the COI sequences …