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I've used kneaddata for some time. It is quite robust with its features. I felt it is more flexible to use than current viral-ngs handlings of quality controls. So maybe `viral-ngs` can borrow `knead…
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In particular, better info about the two database items.
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Hi!
I have mapped my sequencing reads against the [IGC database](https://db.cngb.org/microbiome/genecatalog/genecatalog_human/) (nucleotide sequences), and wanted to run Omixer-RPM using the [GBM D…
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Hi,
I'm new to metaphlan, and trying to run the tutorial. But there was a problem with the first step.
Code: metaphlan SRS014476-Supragingival_plaque.fasta.gz --input_type fasta -o SRS014476-Supragi…
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(copied from https://github.com/sourmash-bio/sourmash/issues/461#issuecomment-1993390314)
Hi Titus @ctb , I don't know whether I could ask the following questions related to this issue, anyway....
…
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I get a comment when running the phylophlan
graphlan_annotate.py \
> --annot graphlan/isolates_annotation.txt \
> output_isolates/RAxML_bestTree.input_isolates_refined.tre \
> graphl…
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The wiki page on profiling shows the output as:
```
sample01 sample04 sample05 sample08
g00001 1 0 1 0
g00002 0 1 1 1
g00003 0 …
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When trying to install in a conda environment:
```
:~$ conda install -c biobakery lefse
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen …
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I am confuse for data import, can i import data in metaphlan2 style?
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For example,
- [x] removal of low-variance features
- [x] removal of low-count features
- [ ] grouping of perfectly co-linear features/removal of identical features
Tagging in @jboconnor13 i…