Is your feature request related to a problem? Please describe.
A standard step of ancient metagenomics work (pathogens, microbiome), is now performing a metagenomic screening i.e. rapid/approximate alignment against a reference database of many genomes at once - typically on the off-target reads of the original host (e.g. host is human, but want to look what bacterial infection killed the person). It would be another good end point of EAGER is a basic OTU table (and some summaries), as initial microbial composition check before downstream analysis outside the scope of EAGER.
This would also be a nice upgrade from EAGER1, for any future publication as it brings EAGER up-to-date with the current state of the aDNA field.
Describe the solution you'd like
Add meta-genomic module.
Suggestions:
- HOPS Pipeline (currently requires a slight modification to the conda recipe to make malt-extract accessible via a environment variable)
- Kraken (@maxibor - would need your input here)
Other things to consider
MALT (used in HOPS) often requires a large amount of MEM/CPUs depending on the database. How to specify this/warn the user?
Is your feature request related to a problem? Please describe.
A standard step of ancient metagenomics work (pathogens, microbiome), is now performing a metagenomic screening i.e. rapid/approximate alignment against a reference database of many genomes at once - typically on the off-target reads of the original host (e.g. host is human, but want to look what bacterial infection killed the person). It would be another good end point of EAGER is a basic OTU table (and some summaries), as initial microbial composition check before downstream analysis outside the scope of EAGER.
This would also be a nice upgrade from EAGER1, for any future publication as it brings EAGER up-to-date with the current state of the aDNA field.
Describe the solution you'd like
Add meta-genomic module.
Suggestions:
Other things to consider
MALT (used in HOPS) often requires a large amount of MEM/CPUs depending on the database. How to specify this/warn the user?