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Hi, I am wondering if there is a functionality to join two kraken output files together?
Thanks,
Tayab Soomro.
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I'm classifying representative sequences of quality controlled and clustered 16S reads with command:
java -jar AlignmentTools.jar pairwise-knn query.fq db.fa
The db file is unaligned prokaryotic sub…
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Hello,
I've been using the SAMSA2 pipeline and it works great for my application.
One thing I've noticed is that the genus/species names reported for Step 5 outputs are parsed using the final tw…
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I'm profiling through several hundred species and noticed that at least one of them throws the following error despite being a valid species name (and having a valid BacDive entry):
```
ERROR: Ill…
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Some genomes downloaded from PATRIC had genes with incorrect genome coordinates. For example, gene id 1313.4609.peg.100 from genome id 1313.4609 from species id Streptococcus_pneumoniae_58285.
This…
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I made a tree and got a root named "cellular organism"
ran
`CanSNPer2 --database bacillus_anthracis_new.db data/*.fasta --summary --save_tree --tmpdir temp/ --strictness 0.8`
and got a warning …
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I am unable to buildDB, initially I suspected it was because the fna files were gunzipped but after un-gzipping them, a new issue arose.
I used the following commands to download a smaller version …
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Hi,
I have this issue at the end of running srst2 using resistance gene database. Can anyone please let me know why this error occurs and how to resolve it?
sh: -c: line 0: syntax error near un…
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The primary output of `ami-phylo` is NEXML and the current output validates against nexml.org.
I propose we use NEXML to aggregate per-OTU logging information.
```
read tree format (e.g. ijsem.x…
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In the 2024-01-25 presentation, it was clear that most of the class finished within 70min, for a planned 120min session.
In addition, the initial workshop exercise starts students with a difficult …