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Running woltka classify as "Step 2: stratified functional profiling" with preserved --outmap in first woltka classify for taxonomy and got this error:
cat ~/plasma_woltka_strat-1.e1315562
Tracebac…
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Following the installation of Anvio (#23) we can now run it by activating the mamba environment `anvio-8`.
Lets create a new directory for the anvio run that we will use as the working dir.
```
m…
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Is there a current plan to include other microorganisms like fungi?
It would most probably involve other tools and databases, but at least for the assembly, spades could work, too.
Is there a wa…
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Hi -
I'm interested in obtaining estimates of relative abundance across all domains of life. Is this possible with sylph? If so, it's unclear to me if that would entail concatenation of pre-built d…
bcpd updated
3 months ago
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Please leave the headers below and replace the relevant text. This will expedite addressing the ticket.
**Name the workflow**
Taxonomic-Profling-Diamond-Megan
**Describe the bug**
The workf…
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### Description of feature
Could you recommend what the current best practices around taxonomic profiling of nanopore data (r10.4.1) are? Many thanks - and thank you for developing this tool.
bcpd updated
5 months ago
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Thanks for developing this new tool. Impressive.
After a quick reading, it seems that your tool use the species specific groups of sequences to do the classification for different species, similar…
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First, all reads are merged.
We skip the CO_ and CH_ as they contain all reads for hostplant respectively.
```
ls -1 05-CLEAN-MERGED/* | paste - - | grep -v "CO_" | grep -v "CH_" > doc/all-clean-re…
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Starting an issue to keep track of this limitation in our current implementations of deduplication and duplicate statistics.
Currently the `CLUMPIFY_PAIRED` process has the comment flag "NB: Will N…
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**Hello, I would like to ask**
Is there any **difference** in algorithm between this and Pathoscope, and is it **more accurate** in identifying pathogenic microorganisms? Is there an advantag…