JohnVollmers
JohnVollmers
The default setting for threads of mmseqs2 is to just use all threads. This is not a safe default, especially if multiple people are working on the same system. One...
with the current recipe, GroopM "installs" without error, BUT is non-functional. I originally thought the problem was the python version, but it is actually the pytables version. GroopM uses a...
Barrnap creates an index file of the query sequence before searching for rRNAs. if this inex already exists, it skips the creation of this index. This can lead to problems,...
Barrnap v.0.9 produces gff-output and (optionally) a fasta output. The fasta output has the coordinates of each rRNA prediciton in the header, but not the evalue of that prediction. The...
I was always wondering (also for rnammer and similar tools) why there always seems to be a strict rule to only search for archaeal OR bacterial rRNAs, but never for...
Your wiki states that the default value for the threads argument is to use all available cpus on the system. That is highly dangerous behaviour and definitively not a good...
When creating Krona charts with `ktImportTaxonomy` you have the option to include "score" values for each entry, and colore the resulting graph based on the average score for all wedges....
```updateTaxonomy.sh``` and ```updateAccessions.sh``` would be most useful in the PATH. However their more generic name can be a problem if other taxonomy-based tools are installed and use the same naming...
Currently you can specify an **absolute** bitscore threshold for determining "best hits" in ```ktClassifyBLAST```. Hits differing from the highest bit-score by more than this value will not be considered. This...
When installing blast via the bioconda channel (```conda install blast``` with "bioconda" already in my channel list), the "newest" version seems to default to v.2.5.0, even though the most current...