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I understand that diamond output read number may be considerably less than diamond input read number, as the output excludes reads for which no alignment is found i.e. excludes "no hit" reads.
How …
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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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### 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-…
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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 …
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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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Dear dada2 enthusiasts,
I'm pretty new to dada2 so I would like to hear some opinions from those who are experts and use dada2 regularly about my issue analysis.
I have tried using filterAndTrim…
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Hello!
I am processing ITS data with DADA2 (primers ITS1F-ITS2). I am following recommendations from this paper (https://www.sciencedirect.com/science/article/pii/S1754504818302800?via%3Dihub) and fo…
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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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Dear Emese,
First of all, thank you for creating this tool and the documentation. They are really helpful. I created a custom database to use with the blast+ command line utility. However, the result…