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I'm trying to use a clustered version of the NR database for taxonomy assignment but am running into some issues. Any assistance would be appreciated.
## Expected Behavior
When running `mmseqs cre…
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Hello,
When testing taxonomy assignment I noticed that the output would change if the order of the sequences in the sequence table was different (this apparently was due to the order in which the f…
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Hi,
I generate a phyloseq file following the Bioconductor Workflow for Microbiome Data Analysis (https://f1000research.com/articles/5-1492/v2). Tree construction was done using dada2 and phangorn p…
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Dear All,
I would like to know is there any option we can use user generated database instead of the default one? I would like to use rrNDB database. https://rrndb.umms.med.umich.edu/static/download/…
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**references**
- White JR, Nagarajan N, Pop M (2009). [Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples](http://www.ploscompbiol.org/article/info%3Ado…
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Brian,
Is there a mechanism for adding in custom annotation types, beyond different blast searches? For instance, what if I wanted to add BUSCO output, or another of the CBS Software reports (for i…
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Thanks for sharing the protocol. I have tried it for some prophage genomes, but most genomes can only have the taxonomic information in "class" level. Is there a way to get species/family level inform…
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It is possible to get the classification for some interesting functional genes:
I want to know both the abundance and the classification for AOA, AOB, nirK/S and nosZ; wonder how can I do this usin…
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**Is your feature request related to a problem? Please describe.**
When the input FASTQ file does not exist, MATAM does not stop properly its execution
**Describe the solution you'd like**
Stop t…
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Hi,
I was wondering if there was going to be a new DADA2-formatted GreenGenes database based on the new release (https://forum.qiime2.org/t/introducing-greengenes2-2022-10/25291)? I was looking thr…