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The machine learning classifiers used for taxonomic assignment usually assume that all taxonomies are equally likely (eg. Wang, 2007). That assumption can be relaxed for `q2-feature-classifier`.
To…
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HI
I was using shapemapper2 for my analysis. We have three sample experiments i.e., denatured, modified, and untreated. I ran the experiments by giving the primer sequences in lowercase in input.fa f…
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Fix bugs identified in first anospp production run
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Hi, I am using stringMLST and I noticed that I got different results for running the same sample more than once. The database changed (updated). What was surprising that some of the assigned ST's in t…
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@nbokulich, @mikerobeson, @BenKaehler - how important do you all think the region-specific classifiers are? My impression is that they offer fairly small classification performance gains relative to t…
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### Description of the bug
Dear authors,
We were trying to use the ampliseq pipeline in sidle mode but get stuck at the NFCORE_AMPLISEQ:AMPLISEQ:SIDLE_WF:SIDLE_DBEXTRACT step.
Looking at the `…
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Hi team
Could you please let me know if this fasta file (screenshot below) work fine for dada2 pipeline to be used instead of silva 1.38? DO you think that is compatible with `assignTaxonomy()`. T…
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Hi,
is this pipeline suited for nanopore data?
kind regards,
T.
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Hello,
I'm wondering if anyone can assist with some issues I'm having re: locus assignment.
Some of my forward primers include ambiguous nucleotides (K, W, R, etc.) and some of the expected STR…
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### Description of the bug
I am recently running the viralrecon 2.6.0 on some sars-cov-2 sequences; I noticed that ivar.tsv output doesn't match with the snpeff. annotated vcf as well as the varian…