Comments (2)
Fastp deduplicate with strict settings & update label to high memory (at least 24G).
Then we can also deduplicate with UMI tools
from viralgenie.
It's not good enough, do look into UMIc and use it to deduplicate our reads or the other tool @LianaKafetzopoulou suggests.
from viralgenie.
Related Issues (20)
- Identify total number of reads after host-removal not just % HOT 1
- Make a conda biocontainer for viralgenie
- Simplify preclustering of contigs up to a certain level HOT 1
- Migrate annotation files to external repo HOT 1
- Refactor readclassifier & preclustering HOT 1
- autodetect paired-end
- Out-of-memory during NETWORK_CLUSTER process on unclassified taxa
- Contig consensus 0 coverage HOT 1
- Include coverage plot in MQC HOT 1
- nf-test
- patch nf-core template
- patch nf-core modules
- Include sspace & cobra for contig extension
- Set default UMI-tools dedup strategy to a non-read counting method
- Vazymolo
- Make a quick start section
- FIx OOM for long contigs
- include option for protein clustering
- Filtering clusters HOT 1
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from viralgenie.