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We have previously discussed adding metagenomics compatibility by running fly in meta mode and doing genome binning.
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I am in the process of determining whether sourmash is the right tool for my metagenomic analyses. I am mostly using ONT data at the moment. Similar to previous posts (e.g. https://github.com/sourmash…
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Hi MGnify team.
Apologies if this is not the correct place to report this issue, but I am interested in getting an protein -> contig -> assembly map and figured I could rely on the [mgy_assemblies.…
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Run TriP canine datasets through metagenomic workflows
nmdc study is nmdc:sty-11-hdd4bf83
db.getCollection("omics_processing_set").find({'part_of':'nmdc:sty-11-hdd4bf83'})
There are 61 datasets. …
aclum updated
2 months ago
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Hello,
Is BESST suitable for scaffolding metagenomics contigs ?
thanks,
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- BBDUK
- HOSTREMOVAL
- MALT/KRAKEN
- MALTEXTRACT
- KRAKENPARSE
## New
- Option: mapped OR unmapped reads to metagenomic screeming
- KRAKENUNIQ
- METAPHLAN3
- PRINSEQ (alternative comple…
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When I run "nextflow pull EBI-Metagenomics/emg-viral-pipeline"
I get error :
Checking EBI-Metagenomics/emg-viral-pipeline ...
Project config file is malformed -- Cause: Compile failed for so…
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### Operating System
Other Linux (please specify below)
### Other Linux
Ubuntu 18.04
### Workflow Version
v2.9.0
### Workflow Execution
EPI2ME Desktop application
### EPI2ME Version
v5.1.10
…
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### Operating System
Ubuntu 22.04
### Other Linux
_No response_
### Workflow Version
v2.9.3-g6636bc9
### Workflow Execution
Command line (Cluster)
### Other workflow execution
_No response_
…
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Hi,
I have a little over 1 million proteins from a metagenome I would like to perform an easy-search on Alphafold/UniProt50. I am running foldseek on Google Cloud so I am fairly flexible on CPUs an…