Any suggestion on metagenomics pipelines for processing shotgun metagenomics whole genome sequencing samples?
I have some shotgun metagenomics gonorrhea samples and I want to use metagenomics pipeline to process the samples and then detect antimicrobial resistance. I looked into few pipelines so far for metagenomics data such as ATLAS, Sunbeam, MetaSUB/CAP2 and nf-core/mag. They have different steps of data processing with different features and tools used.
- Is there a review paper or some documents that compares these pipelines in terms of pros/cons?
- Is there any other pipeline(s) that based on your experience, I can use? or even any pipeline that you think works better among the ones I mentioned?
Any suggestions will be appreciated.
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