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This issue summarises the discussion that emerged at the London hackathon concerning a possible merge with [YAMP](https://github.com/alesssia/YAMP)
While MAG focuses heavily on assembly, YAMP is as…
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### Description of the bug
As suggested by @Midnighter https://nfcore.slack.com/archives/C031QH57DSS/p1673863932137969?thread_ts=1673858047.865519&cid=C031QH57DSS
(i.e. classification - who is the…
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Hi, I'm Jaebeom Kim working on metagenomic classification.
I want to ask a question about reference databases used in the taxonomic binning challenge.
I can find three reference sequences on the C…
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Ultimately we'll want `FeatureTable` and `FeatureData[Taxonomy]` results to use these data in downstream applications. One option would be to use [Bracken](https://ccb.jhu.edu/software/bracken/) to go…
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Hello,
I'm part of a project called the Common Fund Data Ecosystem (CFDE) (https://commonfund.nih.gov/dataecosystem). Our group, under PI Owen White, are the CFDE Coordinating Center. Among other…
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### Description of the bug
Maybe there is a misunderstanding about what particular parameters of the pipeline mean but I think the way setting the parameter `--save_runmerged_reads` currently perform…
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### Description of feature
Add an option to save the quality filtered reads that are input for the assembly and taxonomic profiling sub-pipelines. These would be very useful for use in other pipelin…
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Hello
I am a beginner and I have a question about metagenomic analysis using HiFi PacBio long reads. In short read metagenomics I have seen in some papers who suggest doing taxonomic and functional…
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### Description of the bug
When I attempt to run `nf-core/mag`, the script, immediately after startup, errors with the following unusual output:
```
Is a directory
-- Check script '/ref/djs…
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Hi shenwei356,
Thank you for this very promising tool! Based on your instructions, I was able to build an up-to-date database and have been testing KMCP on some previously characterised metagenomes…