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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…
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After assigning taxa when making the associated bar plot, it would be nice to have the ability to set an "others" group. For example, for taxa that are lower than 1%, group all of them to something li…
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I reviewed the manual annotations file, and overall it looks great. The major things that seem to be missing but could be easily provided, and would be really useful in building search systems, are s…
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Hi!
I am trying to use this package to remove as much contaminants as I can from an already cross contaminated samples.
For context, this data comes from NovaSeq sequencing, so I am working with E…
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Command and output pasted below. Lineages csv attached and reproduced!
```
sourmash tax prepare --taxonomy-csv inputs/sourmash_databases/cheesegenomes.lineages.csv -o tmp.sqldb
== This is sourm…
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In your last paper about HISAT-genotype (https://pubmed.ncbi.nlm.nih.gov/31375807/) you described the algorithm of assignment of HLA allele abundance based on a strategy of Expectation Maximization:
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In my phyloseq object, chloroplast is present as class whereas mitochondria present as family: is it correct taxonomy in phyloseq object?
> ntaxa(physeq)
[1] 67405
> physeq0 ntaxa(physeq0)
[1] …
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The figure produced by plot_tree is missing many family-level labels although most of the taxa contain family-level assignment. Also the placement of the labels were off for several taxa.
![tree](h…
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hi rcedgar,
Thanks for your powerful software.
I have a batch of aa seqs and RdRp already verfied. I try to use palm_annot and palmDB by blastp to annotation the seqs.
I also used your palmsca…
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I was wondering if it makes sense / is straight-forward to use blobtools2 to decontaminate de novo transcriptomes. If so, are there any recommendations that differ from the approaches used for genomes…