There are 3 repositories under pathogen topic.
Rapid large-scale prokaryote pan genome analysis
Finds SNP sites from a multi-FASTA alignment file
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
A tool to circularize genome assemblies
Antimicrobial Resistance Identification By Assembly
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Get assembly statistics from FASTA and FASTQ files
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Python3 scripts to manipulate FASTA and FASTQ files
Repository containing lists of all published ancient metagenomic (and related) samples and libraries
Improve the quality of a denovo assembly by scaffolding and gap filling
de novo virus assembler of Illumina paired reads
Scripts. config, and snakefiles for seasonal-flu nextstrain builds
Nextstrain build for mpox virus
Predict plasmids from uncorrected long read data
A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV rebuilds.
Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
Multilocus sequence typing by blast using the schemes from PubMLST
Assembling the cause of phenotypes and genotypes from NGS data
SaffronTree: Reference free rapid phylogenetic tree construction from raw read data
A set of tools to analyse the output from TraDIS analyses
Minimal colorscheme for vim.
k-mer based Pipeline to identify the Serotype from Illumina NGS reads
Mycobacterial pipeline
PoPS (Pest or Pathogen Spread) R Package
Comparative TraDIS analysis
A data specification for harmonizing One Health AMR pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via a spreadsheet collection template, supported by field and reference guides as well as different curation and new term request SOPs.