Wyler, E., Lauber, C., Manukyan, A., Deter, A., Quedenau, C., Teixeira Alves, L. G., ... & Landthaler, M. (2022). Comprehensive profiling of wastewater viromes by genomic sequencing. bioRxiv, 2022-12.
DOI: https://doi.org/10.1101/2022.12.16.520800
This repository incorporates two pipelines for RNA and DNA samples generated from wastewater:
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Kaiju Pipeline for taxonomy classification:
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CCTyper Pipeline for predicting cas proteins:
- Divide assemblies into chunks with pyfasta.
- CRISPR-Cas gene detection with CRISPRCasTyper.
In addition to preprocessing pipelines, we also provide access to custom scripts for the downstream analysis for both taxonomy classification and Cas protein detection:
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Metagenomic Analysis on taxonomically classified reads:
- taxonomy ranks and lineage with taxizedb.
- Processing and PCA of taxonomy counts.
- Visualize heatmaps with ComplexHeatmap.
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Downstream Analysis on reads associated with CRISPR-Cas genes: