-
Hello Team,
I simulated a shotgun metagenomic Nanopore dataset using NanoSim, containing:
65% bacterial sequences from 32 bacterial species
35% human sequences
For profiling, I created a Sylph…
-
If I add strain information to nodes.dmp and names.dmp, can kmcp perform strain level profiling?
Thanks.
zwh82 updated
10 hours ago
-
Add strainphlan modules & subworkflow to pipeline
-
I suggest using the poreCov pipeline as the backend for SARS-CoV-2 wastewater lineage deconvolution from nanopore long reads. You already added `freyja` ( #274 #270), which is great as the current com…
-
Hey there,
I am encountering the following error when running the panphlan_profiling.py script:
```
...
STEP 2. Create coverage matrix
[I] Reading mapping result file: MP3_TONGUE_DNA_Rothia_…
-
### This issue occurs when only Valkyrien Skies and addons are installed and no other mods
- [X] I have tested this issue and it occurs when no other mods are installed
### Minecraft Version
…
-
I get this error after the step 3 (strain presence/absence) during profiling when I try a different threshold. It was working the first time I tried it. What can be the issue? I used:
python panph…
-
request sent privately:
>I am interested in finding strains of an bacteria (say E. Coli) in ~100 metagenomes. What’s the best way to do this?
Misc thoughts:
* suggest adopting a triage workflow…
ctb updated
10 months ago
-
From `centrifuger` paper, I found it can perform strain level profiling. How to achieve it? Is this achieved by assigning the `seqID` column in the `classification.tsv` file to the corresponding strai…
-
Hi,
I notice that while --similarity cutoff is by default mention as 0.95 it actually uses 0.80 cutoff while merging and clustering results from samples. I feel 0.80 is bit conservative. What do y…