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Dear all,
I think I understood this pipeline and I already have used similar software [PanPhlAn] that goes through a similar path (build pangenome, compare reads, etc). I now want to use StrainGE,…
drelo updated
3 years ago
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I group here a discussion on how to assemble complex metagenomes, e.g. soil.
Spades is probably still the best assembler even for complex metagenomes (https://twitter.com/ryneches/status/1352732023…
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I ran metaQUAST without providing any references to allow it run its reference inference pipeline with the SILVA database, however it seems only three genomes were downloaded, of of them itself being …
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Dear developers,
Thank you for implementing various plasmid detection tools.
I'm comparing different plasmid software's outcomes and I have seen that SCAPP Uses Plasclass's classifier already. In th…
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Hi,
I'm running the HiFi-MAG-Pipeline. The pipeline exit when running RunGTDBTkIndividual. As the error message said, I check the required file in *4-checkm-summary* folder, and it shows that *w2.b…
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Hi David,
I've managed to run OGT prediction on my own metagenome assembled genomes (MAGs), using the models present in the data/prediction_demo/regression_models/ directory.
The results seem to m…
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I don't know if you have thought about that question. Can I use to run VAMB to bin eukaryotes? Or another way around is there something that this should't work?
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Shane, Paul and Bin and team will document current workflows and link to their documentation in this issue. This information will be used by Yuri for the design document.
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Any plans on creating a reference database of bacteria and archaea?
If no, can you please provide the details on how you constructed the bacterial reference database? I can't find any info on that…
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Dear Francisco,
Recently, I have tried to use your pipeline to analyse some metagenome data. For the bin, i found I can only get about 30 MAGs of high quality (completeness > 90% by checkM). So I am …