Projects in Awesome Lists tagged with pathogen
A curated list of projects in awesome lists tagged with pathogen .
https://github.com/nextstrain/ncov
Nextstrain build for SARS-CoV-2
ncov nextstrain pathogen sars-cov-2
Last synced: 14 May 2025
https://github.com/sanger-pathogens/roary
Rapid large-scale prokaryote pan genome analysis
bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing
Last synced: 21 Oct 2025
https://github.com/ncbi/amr
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
antibiotic-resistance bioinformatics genomics pathogen
Last synced: 10 Oct 2025
https://github.com/sanger-pathogens/Roary
Rapid large-scale prokaryote pan genome analysis
bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing
Last synced: 02 Apr 2025
https://github.com/sanger-pathogens/snp-sites
Finds SNP sites from a multi-FASTA alignment file
bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing
Last synced: 30 Dec 2025
https://github.com/nextstrain/mpox
Nextstrain build for mpox virus
augur auspice bioinformatics genbank genomic-epidemiology metadata monkeypox mpox nextstrain pathogen phylogenetics pipeline virus-evolution
Last synced: 09 May 2025
https://github.com/nextstrain/seasonal-flu
Scripts. config, and snakefiles for seasonal-flu nextstrain builds
Last synced: 09 Apr 2025
https://github.com/nextstrain/ncov-ingest
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.
bash genbank gisaid ncov nextstrain pathogen python sars-cov-2
Last synced: 19 Aug 2025
https://github.com/sanger-pathogens/mlst_check
Multilocus sequence typing by blast using the schemes from PubMLST
bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing
Last synced: 21 Feb 2026
https://github.com/nextstrain/avian-flu
Nextstrain build for avian influenza viruses
Last synced: 06 Oct 2025
https://github.com/szorfein/darkest-space
Minimal colorscheme for vim.
angular-2 colorscheme green linux meteor pathogen purple vim vundle
Last synced: 27 Oct 2025
https://github.com/chgibb/PHAT
Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform
alignment analysis bam bam-files bioinformatics bioinformatics-analysis bioinformatics-tool circos circos-graphs circos-plot dna electron host next-generation-sequencing ngs pathogen phat quality-control snps visualization
Last synced: 05 May 2025
https://github.com/ncbi/stxtyper
StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.
bioinformatics bioinformatics-tool escherichia-coli genomics pathogen virulence-genes
Last synced: 24 Oct 2025
https://github.com/ncsu-landscape-dynamics/rpops
PoPS (Pest or Pathogen Spread) R Package
insect modeling pathogen pathogen-spread pest pests pops simulation
Last synced: 12 Jan 2026
https://github.com/nextstrain/forecasts-ncov
SARS-CoV-2 variant growth rates and frequency forecasts
bioinformatics forecasts nextstrain pango-lineages pathogen sars-cov-2 sars-cov-2-variants
Last synced: 19 Aug 2025
https://github.com/nextstrain/rsv
Workflow for RSV analyses on Nextstrain.org
Last synced: 19 Aug 2025
https://github.com/ccdmb/catastrophy
CATAStrophy predicts filamentous plant pathogen lifestyle characteristics based on their CAZyme composition.
bioinformatics fungi pathogen pathogenomics trophic-interactions
Last synced: 08 Apr 2026
https://github.com/ncsu-landscape-dynamics/pops-core
PoPS Core: C++ library for the Pest or Pathogen Spread Model
epidemiology hacktoberfest model pathogen pathogen-spread pest pests pops pops-library simulation spread
Last synced: 03 Apr 2026
https://github.com/chonglc/minimalsetofviralpeptidome-uniqmin
An alignment-independent tool for the study of pathogen sequence diversity
alignment-independent minimal-set pathogen proteome python3 sequence-diversity virus
Last synced: 27 Feb 2026
https://github.com/kaworu/vim-coccinelle
pathogen friendly vim syntax files for coccinelle
Last synced: 15 Mar 2025
https://github.com/nextstrain/wnv
the repository used to build West Nile Virus for nextstrain
Last synced: 19 Aug 2025
https://github.com/stefanoschrs/vim
Vim Configuration
guitar-tabs nerdtree pathogen syntactic vim vim-airline vim-go vim-javascript vim-nerdtree-tabs vim-node vimrc
Last synced: 16 Mar 2025
https://github.com/kwakwaversal/vimfiles
My ~/.vim directory. All hail vim.
Last synced: 28 Feb 2025
https://github.com/nextstrain/seasonal-cov
Nextstrain build for seasonal coronaviruses
Last synced: 10 Jun 2025
https://github.com/akshayparopkari/discover_tfbs
Discover transcription factor (TF) binding specificities/sites (TFBS) using binding site motif sequence and structural information.
bash binding-sites biofilm bioinformatics biology candida-albicans computational-biology fungal machine-learning pathogen python r scripting transcription-factors
Last synced: 25 Jan 2026
https://github.com/achris07/vim-config
Just a repository with my VIM configuration file and plugins, for others to use and for me to clone on new computers.
pathogen vim vim-configuration viml
Last synced: 05 Apr 2025
