Comments (3)
Hi Greg
OK! Maybe it's not a big issue with the smaller contigs then. We did not exactly optimise the hyperparamaters of the vamb binner for pure viral-contigs subset, instead it's optimised to handle the simultaneous presence of bacterial or contigs from other entities, but so far in our tests it has performed pretty well for pure virus subsets.
Remember to do binsplits of your VAMB clusters by the sample identifier in your contigs (also advised in the VAMB repo).
Wishing you all the best with your viral metagenomic research! :-)
Best,
Joachim
from phamb.
Hi Greg
My only worry with this approach is that you might miss out on some contigs (especially smaller ones < 5000 bp) that might belong to a virus and contain a limited number of viral genes, thus they will not be picked up by VIBRANT in the process and be discarded.
Nevertheless, your approach is totally feasible and should work fine. In the paper we did benchmarks on contig-subsets derived from viruses only (this will sort of correspond to your contig-input to vamb) and it really put the binning on "steroids".
Best,
Joachim
from phamb.
Hi Joachim
Thanks a lot for the quick response, FYI the default for Vibrant to consider contigs is 1kb and 4 ORFs.
Best
Greg
from phamb.
Related Issues (20)
- modified header names in PHAMB HOT 4
- Versioned release package for Phamb HOT 16
- Parsing deepvirfinder line 512, in _parse_dvf_row contig_name, length, score, pvalue = line[:-1].split() HOT 2
- contig length HOT 1
- Update shebang lines in phamb python scripts HOT 2
- High number of bacterial genes in phamb assembled bins HOT 3
- split_contigs.py produces empty files HOT 1
- Can PHAMB output comparable performance on environmental metagenome compared to gut metagenome HOT 1
- split_contigs.py produces empty files HOT 2
- how to evaluate the bin-annotations? HOT 1
- What are the criteria of RF model HOT 2
- The predicted 'viral' number in 'vambbins_RF_predictions.txt' is inconsistent with the actual number in 'vamb_bins.1.fna'? HOT 1
- Binning question, how to use vamb? HOT 7
- 'run_RF.py' operation problem HOT 1
- how to get the file 'clusters.tsv' ?
- VAE or AAE? HOT 1
- How to Run - not in parallel - quick and dirty HOT 1
- interpret the results of RF model
- Can PHAMB be used directly for Virome analysis (enrichment of viral particles followed by sequencing) HOT 2
- category of viruses identified by PHAMB ?
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