viral_surveillance
Viral surveillance analysis geared towards the Illumina viral surveillance panel.
Overview of Pipeline
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Read QC & trimming
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Human/host depletion (alignment to human)
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Taxonomic classification (virus detection)
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Reference alignment for detected viruses
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Variant calling
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Consensus genome generation
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Phylogenetic placement
Each step is a task with a Docker container specified.
Notes
- This workflow assumes pre-computed human and viral reference indices
(
This is a companion discussion topic for the original entry at github.com/ranlib/viral_surveillance/viral_surveillance