Comments (2)
Hi - Thanks for the kind words!
First, the PHAMB approach was designed with Bulk metagenomics in mind, but the binning process and approach should work all the same on VLPs. However, if you are working with VLP samples, which usually contain a lot of random small bacterial chromosomal fragments/Junk, there might be a lot of value in performing a prefiltering step.
I would suggest:
- Identify virus like contigs for each sample using a more recent and fast tool such as GeNomad (https://github.com/apcamargo/genomad). This will also save a lot of time for the subsequent steps.
- Use these contigs as your starting point (i.e. contigs.fna.gz) for running VAMB and then PHAMB.
Hope this approach is helpful!
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Thanks for the advice, I'll try the workflow you recommend!
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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
- category of viruses identified by PHAMB ?
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