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License: MIT License
Atavistic processing of metagenomics data.
License: MIT License
At the moment we have a simple assembly approach:
There is another approach we might consider:
Each approach has its pros and cons, of course, but the 2nd approach might remove all the redundant stuff in all the libraries quite quickly.
Creating a link to a file modifies its time of last data modification, human-readable
(to test, check stat -c '%w %x %y %z' filename
)
and thus snakemake deems necessary to rerun the files because earlier files appear older than subsequent files.
Solution: make all links immediately after creation?
We need to revive the super-focus
taxonomy because it is based on protein sequence similarity.
There are a couple of places where we use scripts/renumber_merge_fasta.py
and rename fasta/q files. We could do this more efficiently with seqtk rename
and we already have seqtk
as a dependency.
In some places we use taxon kit and some places we use my taxonomy SQL database.
Unify these into a common location
Use the mags and reads to separate out strain level resolution.
Add AMRfinder plus to atavide
The tool is found at AMRFinderPlus
You can find the tool at ncbi-amrfinderplus
See their [wiki](https://github.com/ncbi/amr/wiki/Install-with-bioconda]
Note: we need to consider adding protein calls (e.g. prokka?) and then using the AMRfinder plus HMMs. Note that genbank_to might help with the AMR finder GFF input
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