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Hi,
I see that CLAP is designed to run on eukaryote genomes.
How to adapt it to run on bacteria?
I changed `make_annotation.sh` by adding species _escherichia_coli_k_12_ and adjusted ftp site and…
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**V doctor:**
```
OS: macos, macOS, 11.6, 20G165
Processor: 4 cpus, 64bit, little endian, Intel(R) Core(TM) i5-6267U CPU @ 2.90GHz
CC version: Apple clang version 13.0.0 (clang-1300.0.29.3)
g…
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Hi everyone,
I was using GTDB-Tk/2.3.2, and after updating to GTDB-Tk/2.4.0, some Spirochaetota bacterial species started clustering far from each other in the phylogenetic tree (shown in dark gree…
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The Greengenes-style taxonomic lineage file format is widely used in microbiomics, such as QIIME 2, GTDB-tk, MetaPhlAn, etc. It would be good to let the user append taxonomic annotations of contigs by…
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When running `build_kraken`, the `add_existing` process fails with messages such as
```
rsync_from_ncbi.pl: unexpected FTP path (new server?) for https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/7…
cschu updated
9 months ago
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Hi Diener,
I tried to run qiime micom build and had the error in below:
version info: …
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Hello,
I am trying to import a file into phyloseq that does not look like the files in the tutorials. The samples are repeated mulitple times, as are the sequences. I would like to treat the sequence…
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`ngd --taxids` seems to require `gimme_taxa.py` have the `-j`. Not sure if you want to update the documentation or one of the scripts?
```
$ gimme_taxa.py -o taxids.txt Hyphomicrobiales
$ ngd --d…
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Hi @zachary-foster!
Thanks so much for your package!
I'm trying to parse the taxonomic information output from QIIME, and I am wondering the best way to do this. With command line tools I have a…
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The `aggregate_*` methods, when dealing with missing taxonomic information return the entire row where there is information combined as shown below.
```
library(jeevanuDB)
library(microbiome)
…