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Hi and hope all is well!
I wanted to inquire about the conda installation timeline. I know that PPR-Meta is not conda-installable which is why you need to withhold the conda implementation. I want…
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Hi,
I have a set of assemblies generated from metaSPAdes, and am getting a "KeyError" for only some of them when running VIBRANT. The contig names do not have any special characters or spaces. Thes…
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Hi,
I have recently tested haploflow on a complex metagenomics dataset, and it seems to be performing very well compared to other tools in producing correctly assembled viral contigs. For testing, I…
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Hi, and many thanks for the excellent annotation tool. I have a query regarding viral AMG annotation. I have a bunch of viral contigs identified through metagenomics. The contigs were cleaned using C…
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Hi!
I am currently working on the IDseq metagenomics platform to identify mapped reads to SARS-CoV-2. Basically my project consists on the sequencing of all reads from a clinical samples with COVID-…
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We should have convenience functions for building kraken, diamond, and metagenomic bwa databases, accessible as CLI subcommands of `metagenomics.py`, similar to the [`taxon_filter.py`](https://viral-n…
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I've used kneaddata for some time. It is quite robust with its features. I felt it is more flexible to use than current viral-ngs handlings of quality controls. So maybe `viral-ngs` can borrow `knead…
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### Description of feature
Adding 2 classifier approaches
Centrifuge and metaPhlan2
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It's not clear why this threshold was implemented and what kinds of situations it's supposed to be help with.
It seems like it would accidentally exclude certain kmers from subtype calling if the …
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