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Add modules outlined in the pipeline proposal #8
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#6 PR draft to start adding modules |
For WGS data for assembly, GenomeScope (https://github.com/nf-core/modules/blob/master/modules/nf-core/genomescope2/main.nf). The database is built using Meryl ( also on nf-core ). But there is also a container only version that's a little bit faster and has extra tools that might be useful (https://github.com/nf-core/modules/blob/master/modules/nf-core/genescopefk/main.nf) |
I've used Another option would be Picard (https://gatk.broadinstitute.org/hc/en-us/articles/360037591931-EstimateLibraryComplexity-Picard). I've never used it, and for the applications I worry about library complexity (HiC) the tool I use (pairtools) implemented it's own complexity estimate, so I have no need. There's no nf-core module for it as far as I can see. |
@remiolsen any idea why |
I'm fairly certain I used to see this error most commonly - and I quote from the preseq manual
And setting the step |
Closed #6 due to being too broad and unspecific. Feel free to start new PRs addressing more specific implementations. |
Functionalities and modules
Mentioned in the pipeline proposal
primaryQC_pipeline_proposal.pdf
Pipeline proposal Slack thread
Standard QC
seqkit watch
seqfu check
seqfu metadata
seqfu merge
Duplication + Complexity
Adapter and Artifact detection
Contamination detection
Mentioned in the pipeline Slack channel
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