> For the complete documentation index, see [llms.txt](https://cgps.gitbook.io/pathogenwatch/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools.md).

# Technical Descriptions of Analysis Tools

- [Genome Assembly](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/genome-assembly.md)
- [Short Read Assembly](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/genome-assembly/short-read-assembly.md): How Pathogenwatch assembles short read Illumina data
- [Assigning species with Speciator](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/speciator.md): Species assignment tool in Pathogenwatch
- [Assembly QC](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/assembly-qc.md)
- [Lineage Assignment & Genotyping Methods](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping.md)
- [cgMLST](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/cgmlst.md)
- [Genotyphi](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/genotyphi.md)
- [Geno7PET](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/geno7pet.md): Sublineage assignments for Vibrio cholerae 7PET pandemic strains
- [HierCC](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/finding-hiercc-codes-with-hclink.md): Linking Enterobase HierCC clusters using the hclink software
- [Kleborate](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/kleborate.md): Klebsiella comprehensive AMR and typing analysis software.
- [Klebsiella LIN Codes](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/klebsiella-lin-codes.md): The Pathogenwatch LIN code tool infers Klebsiella lineage codes based on references from the Pasteur/PubMLST resource.
- [MLST](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/mlst.md)
- [NG-MAST](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/ng-mast.md)
- [NG-STAR](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/ng-star.md): Resistance-based typing of Neisseria gonorrhoeae
- [Pangolin](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/pangolin.md): SARS-CoV-2 lineage assignment tool
- [PopPUNK](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/poppunk.md): S. pneumoniae GPSC strain assignment
- [SARS-CoV-2 Notable Mutations](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/sars-cov-2-notable-mutations.md): Identification of mutations described in the Type Variants database
- [Vista](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/vista.md): Virulence and genotype annotation tool for Vibio cholerae
- [Antimicrobial Resistance Prediction](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/antimicrobial-resistance-prediction.md): Links to the documentation for the AMR tools in Pathogenwatch and currently annotated species.
- [Pathogenwatch AMR](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/antimicrobial-resistance-prediction/pw-amr.md): The Pathogenwatch AMR prediction library and pipeline.
- [Kleborate AMR](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/antimicrobial-resistance-prediction/kleborate.md)
- [SPN-PBP-AMR](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/antimicrobial-resistance-prediction/spn-pbp-amr.md): Analysis of the Streptococcus pneumoniae PBPs and inferred MICs.
- [Resfinder](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/antimicrobial-resistance-prediction/resfinder.md): About the Resfinder software and integration in Pathogenwatch
- [Trees, Clustering, and Context Search](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search.md)
- [Core Genome Tree](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/core-genome-tree.md)
- [About SNP-based trees](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/core-genome-tree/about-snp-based-trees.md)
- [Core Assignment](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/core-genome-tree/core-assignment.md)
- [Core Filter](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/core-genome-tree/core-filter.md)
- [Reference Assignment](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/core-genome-tree/reference-assignment.md)
- [Tree Construction](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/core-genome-tree/tree-construction.md)
- [cgMLST Clustering & Context Searching](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/cgmlst-clustering.md)
- [SARS-CoV-2 Genome Tree](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/sars-cov-2-genome-tree.md): How SARS-CoV-2 trees are constructed in Pathogenwatch.
- [cgMLST Tree](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/cgmlst-tree.md): How cgMLST profile-based trees are constructed
- [Serotyping](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/serotyping.md)
- [Kaptive](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/serotyping/kaptive.md): A tool for typing the surface polysaccharide loci of Klebsiella and A. baumanii
- [SeroBA](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/serotyping/seroba.md)
- [SISTR](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/serotyping/sistr.md)
- [ECTyper](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/serotyping/ectyper.md): About the ECTyper serotyping tool
- [Virulence](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/virulence.md): Virulence annotation tools in Pathogenwatch.
- [STECFinder](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/virulence/stecfinder.md): Shiga toxin genotyping
- [VirulenceFinder](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/virulence/virulencefinder.md): Virulence gene annotation
- [BIGSdb schemes](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/virulence/bigsdb-schemes.md): Pathogenwatch supports integrating virulence schemes from BigsDB
- [Plasmid Annotation](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/plasmid-annotation.md)
- [Plasmidfinder](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/plasmid-annotation/plasmidfinder.md): Identification and typing of plasmid replicons in whole-genome sequencing (WGS).
- [Change log](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/change-log.md)