Comments (4)
Hello Guowei
Like with bacterial MAGs, the sequential order of the contigs in a viral bin/viral MAG is not known. Unless you find a reference genome to guide how to put the genome/contigs puzzle together, even though mosaicism in viruses may hinder this effort. The contigs are, by choice, not connected by gaps like "XXX" or some other accepted DNA character in fasta-files as it might mess up the viral evaluation machinery of CheckV.
Best,
Joachim
from phamb.
Hi Barbara
The output produced by the workflow concatenates the contigs of a bin into one sequence that can be evaluated with CheckV directly - so yes you input that single file with checkV to evaluate the quality of the predicted viral bin :-)
Best,
Joachim
from phamb.
Hello Joachim,
Could you please talk more about the concatenation of sequences in a bin? How does the program perform it? By what standard?
Thank you,
Guowei
from phamb.
No activity on this one, closing it.
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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