add more content from doc

_data/tool_and_resource_list.yml

@@ -1142,3 +1142,57 @@
   name: COVID19 Disease Map
   url: https://covid19map.elixir-luxembourg.org/
   regsitry:
+- description: Freyja is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference).
+  id: freyja
+  name: Freyja
+  url: https://github.com/andersen-lab/Freyja
+  regsitry:
+    biotools: freyja
+- description: The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons.
+  id: cojac
+  name: COJAC
+  url: https://github.com/cbg-ethz/cojac
+  regsitry:
+    biotools: cojac
+- description: Lineagespot is a framework written in R, and aims to identify SARS-CoV-2 related mutations based on a single (or a list) of variant(s) file(s).
+  id: lineagespot
+  name: Lineagespot
+  url: https://github.com/BiodataAnalysisGroup/lineagespot
+  regsitry:
+    biotools: lineagespot
+- description: Kallisto is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
+  id: kallisto
+  name: Kallisto
+  url: https://pachterlab.github.io/kallisto/about.html
+  regsitry:
+    biotools: kallisto
+- description: PiGx SARS-CoV-2 is a pipeline for analysing data from sequenced wastewater samples and identifying given lineages of SARS-CoV-2.
+  id: pigxs
+  name: PiGx SARS-CoV-2 Wastewater Sequencing Pipeline
+  url: https://github.com/BIMSBbioinfo/pigx_sars-cov-2
+  regsitry:
+- description: A GitHub repository from the CBG-ETHZ group offering tools for detecting SARS-CoV-2 variants in Switzerland.
+  id: cowwid
+  name: COWWID
+  url: https://github.com/cbg-ethz/cowwid
+  regsitry:
+- description: A SARS-CoV-2 Contextual Data Specification from PHA4GE.
+  id: sars-pha4ge
+  name: SARS-CoV-2 Contextual Data Specification
+  url: https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification
+  regsitry:
+- description: A data model to improve wastewater surveillance through interoperable data.
+  id: phes-odm
+  name: PHES-ODM
+  url: https://github.com/Big-Life-Lab/PHES-ODM
+  regsitry:
+- description: A pipeline for lineage abundance estimation from wastewater sequencing data.
+  id: vlq
+  name: VLQ
+  url: https://github.com/baymlab/wastewater_analysis
+  regsitry:
+- description: CFSAN Wastewater Analysis Pipeline to estimate the percentage of SARS-CoV-2 variants in a sample.
+  id: c-wap
+  name: C-WAP
+  url: https://github.com/CFSAN-Biostatistics/C-WAP
+  regsitry:

data-analysis/pathogen-characterisation.md

@@ -221,4 +221,24 @@ Even though the considerations for this specific field are very similar to the o
 ### Existing approaches
 
 Several tools and workflows have been developed or adapted for the analysis of wastewater data, especially in the context of SARS-CoV-2 surveillance:
- - Specific Tools for SARS-CoV-2
+ - Specific Tools for SARS-CoV-2: Certain tools (such as {% tool "freyja"%}, {% tool "cojac"%}, and {% tool "lineagespot" %}) are specifically designed for analysing SARS-CoV-2 data, providing capabilities such as variant detection and lineage tracking.
+ - Repurposed Tools: Originally developed for other types of genomic data, tools like {% tool "kallisto" %} or {% tool "kraken2" %}, have been successfully applied to wastewater data analysis, offering high performance in read alignment and taxonomic classification.
+- In addition, here are several bioinformatics protocols and solutions that could be used in the context of wastewater NGS data analysis.
+  - Tools and repositories:
+    - {% tool "pigxs" %}: provides a comprehensive solution for sequencing and analysing SARS-CoV-2 in wastewater.
+    - Detection of SARS-CoV-2 variants in Switzerland by genomic analysis of wastewater samples [medRxiv](https://www.medrxiv.org/content/10.1101/2021.01.08.21249379v2): COWWID: A GitHub repository from the CBG-ETHZ group offering tools for detecting SARS-CoV-2 variants in Switzerland
+    - [CDC Module 2.7](https://www.cdc.gov/amd/training/covid-toolkit/module2-7.html): Wastewater based variant tracking for SARS-CoV-2
+    - The Public Health Alliance for Genomic Epidemiology GitHub organization makes available a mapping to the {% tool "european-nucleotide-archive" %}: {% tool "sars-pha4ge" %}
+    - {% tool "phes-odm" %} as an open data model for wastewater surveillance
+    - Viral Lineage Quantification (VLQ), Kallisto-Approach: [Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02805-9) and corresponding repository at {% tool "vlq" %}
+  - [Performance benchmark of tools](https://peerj.com/articles/14596/), evaluating tools like Kraken2, Kallisto, Freyja, implemented in C-WAP pipeline. , implemented in {% tool "c-wap" %}
+  - Wastewater quality control workflow in GalaxyTrakr [(SSquAWK4)](dx.doi.org/10.17504/protocols.io.kxygxzk5dv8j/v9). Further quality control aspects are discussed in the [Quality Control - Pathogen Characterisation page](/quality-control/pathogen-characterisation)
+  - ECDC [Guidance document](https://www.ecdc.europa.eu/sites/default/files/documents/Guidance-for-representative-and-targeted-genomic-SARS-CoV-2-monitoring-updated-with%20erratum-20-May-2021.pdf) for representative and targeted genomic SARS-CoV-2 monitoring
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