pathogen
There are 3 repositories under pathogen topic.
sanger-pathogens / Roary
Rapid large-scale prokaryote pan genome analysis
Language:Perl 296ncbi / amr
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
Language:C++ 242Artemis 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
Language:Java 227Finds SNP sites from a multi-FASTA alignment file
Language:C 227A tool to circularize genome assemblies
Language:Python 218Antimicrobial Resistance Identification By Assembly
Language:Python 155nickjcroucher / gubbins
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Language:Python 154- pathongs
Get assembly statistics from FASTA and FASTQ files
Language:C++ 107nf-core / taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Language:Nextflow 93Python3 scripts to manipulate FASTA and FASTQ files
Language:Python 68- Language:Jupyter Notebook 64
- AncientMetagenomeDir
SPAAM-community / AncientMetagenomeDir
Repository containing lists of all published ancient metagenomic (and related) samples and libraries
Language:HTML 63 Improve the quality of a denovo assembly by scaffolding and gap filling
Language:Perl 53de novo virus assembler of Illumina paired reads
Language:Python 52andrewjpage / tiptoft
Predict plasmids from uncorrected long read data
Language:Python 38Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
Language:Python 29Assembling the cause of phenotypes and genotypes from NGS data
Language:Python 29Multilocus sequence typing by blast using the schemes from PubMLST
Language:Perl 25SaffronTree: Reference free rapid phylogenetic tree construction from raw read data
Language:Python 23A set of tools to analyse the output from TraDIS analyses
Language:Perl 20szorfein / darkest-space
Minimal colorscheme for vim.
Language:Vim Script 19chgibb / PHAT
Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform
Language:TypeScript 17k-mer based Pipeline to identify the Serotype from Illumina NGS reads
Language:Python 15Pathogen-Genomics-Cymru / lodestone
Mycobacterial pipeline
Language:Python 12- rpops
ncsu-landscape-dynamics / rpops
PoPS (Pest or Pathogen Spread) R Package
Language:R 10 DiseaseOntology / PathogenTransmissionOntology
The Pathogen Transmission Ontology describes the transmission methods of human disease pathogens from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles.
- Language:JavaScript 7
quadram-institute-bioscience / albatradis
Comparative TraDIS analysis
Language:Gnuplot 7ChongLC / MinimalSetofViralPeptidome-UNIQmin
An alignment-independent tool for the study of pathogen sequence diversity
Language:Python 6cidgoh / GRDI_AMR_One_Health
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.
NewLunarFire / wla-vim
WLA Assembly (6502, 65C02, 65816) syntax highlighting
Language:Vim Script 6- Language:Vim Script 6
ldmcdaniel / dotfiles
My dotfiles Installation with Interactive Menu
Language:Shell 5PoPS Core: C++ library for the Pest or Pathogen Spread Model
Language:C++ 5
