Pipelines and Scripts for Wyler, E. et al. 2024

Wyler, E., Lauber, C., Manukyan, A., Deter, A., Quedenau, C., Alves, L. G. T., ... & Landthaler, M. (2024). Pathogen dynamics and discovery of novel viruses and enzymes by deep nucleic acid sequencing of wastewater. Environment International, 108875.

DOI: https://doi.org/10.1016/j.envint.2024.108875

This repository incorporates two pipelines for RNA and DNA samples generated from wastewater:

• Kaiju Pipeline for taxonomy classification:

  • Duplicate removal of reads with CD-HIT.
  • Taxonomy classification and annotation with Kaiju.
  • Custom R scripts for summarizing annotated reads per sample.

• 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:

• Metagenomic Analysis on taxonomically classified reads:

  • taxonomy ranks and lineage with taxizedb.
  • Processing and PCA of taxonomy counts.
  • Visualize heatmaps with ComplexHeatmap.

• Downstream Analysis on reads associated with CRISPR-Cas genes:

  • Clustering open reading frames (ORFs) with CD-HIT.
  • Aligning ORFs to NR database in NCBI with rBLAST.
  • Protein embeddings of ORFs using ProtTrans.