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I group here a discussion on how to assemble complex metagenomes, e.g. soil.
Spades is probably still the best assembler even for complex metagenomes (https://twitter.com/ryneches/status/1352732023…
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1. What is the topic of your lesson or lesson proposal?
Analysis of data related to microbial communities from diverse environments. Specifically, this lesson will focus on analysis of "amplicon" d…
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This is currently in the portal repo. Should we consider something like gravatar? Unsure if ORCID provides public access to a profile image but that might be ideal.
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Dear Benjamin,
first of all: thanks a lot for providing the DADA2 tutorial for assigning 16S rRNA based taxonomy, I learned a lot and appreciate your work very much.
I have one question regardin…
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Hi
I have tried all possible versions of Silva 138 V3-V4 classifiers generated using three different dereplicating mode "uniq" "majority" and "super" in RESCRIPt to classify 16s sequences for mock…
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Tagging @ryanarndtcm and @HaroldDavis3 for links to their ideas.
Everyone else please feel free to share your ideas as well!
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Hello,
I am running optcom on different communities with `sol=com.optcom(strategy='original', min_growth=0.0, fluxes=False, pfba=True) ` and I would like to export automatically the growth rates of a…
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Hi DADA2 developers,
I have been using MiSeq so far, but recently my group bought iSeq and try to analyze iSeq sequence data by DADA2. iSeq generates basically the same outputs as MiSeq does, but I…
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easy reproductible test
```
[gensoft@d37c193b0f41 1.44.3]$ mkdir foo
[gensoft@d37c193b0f41 1.44.3]$ cat > foo/foo.fasta seq
> ATGC
> EOT
[gensoft@d37c193b0f41 1.44.3]$ chmod 555 foo
[gensoft…
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I am perhaps out of my depth but wonder whether this could be rephrased as "molecular [data?] studies" - I'm thinking e.g. of the 'RNA viruses' whose genomes will be made of RNA rather than DNA. To be…