nextstrain/ncov

Nextstrain build for SARS-CoV-2

Language: Python - Size: 28.4 MB - Last synced at: about 11 hours ago - Pushed at: about 12 hours ago - Stars: 1,353 - Forks: 406

SPAAM-community/AncientMetagenomeDir

Repository containing lists of all published ancient metagenomic (and related) samples and libraries

Language: HTML - Size: 165 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 72 - Forks: 33

nextstrain/seasonal-flu

Scripts. config, and snakefiles for seasonal-flu nextstrain builds

Language: Python - Size: 2.48 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 49 - Forks: 28

ncbi/amr

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

Language: C++ - Size: 1.67 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 302 - Forks: 44

nextstrain/rsv

Workflow for RSV analyses on Nextstrain.org

Language: Python - Size: 9.72 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 8 - Forks: 4

xiaoli-dong/pathogenseq

Pathogen whole genome sequence (WGS) data analysis pipeline

Language: Nextflow - Size: 3.62 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 2 - Forks: 1

nextstrain/zika

Nextstrain build for Zika virus

Language: Python - Size: 381 KB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 8 - Forks: 10

nextstrain/hmpv

Human metapneumovirus pathogen build

Language: Python - Size: 3.04 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 0 - Forks: 0

ncbi/stxtyper

StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.

Language: C++ - Size: 979 KB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 13 - Forks: 5

nf-core/taxprofiler

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

Language: Nextflow - Size: 15.8 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 142 - Forks: 48

nextstrain/yellow-fever

Language: Python - Size: 5.28 MB - Last synced at: 17 days ago - Pushed at: 29 days ago - Stars: 1 - Forks: 4

sanger-pathogens/Roary

Rapid large-scale prokaryote pan genome analysis

Language: Perl - Size: 17.7 MB - Last synced at: 22 days ago - Pushed at: about 3 years ago - Stars: 340 - Forks: 190

sanger-pathogens/circlator

A tool to circularize genome assemblies

Language: Python - Size: 25.7 MB - Last synced at: 2 days ago - Pushed at: about 1 year ago - Stars: 240 - Forks: 57

nickjcroucher/gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Language: Python - Size: 9.69 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 184 - Forks: 53

nextstrain/measles

Nextstrain build for measles virus

Language: Python - Size: 8.39 MB - Last synced at: 17 days ago - Pushed at: 26 days ago - Stars: 1 - Forks: 7

nextstrain/WNV

the repository used to build West Nile Virus for nextstrain

Language: Python - Size: 12.2 MB - Last synced at: 17 days ago - Pushed at: 28 days ago - Stars: 4 - Forks: 1

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.

Language: Python - Size: 402 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 36 - Forks: 20

ncsu-landscape-dynamics/rpops

PoPS (Pest or Pathogen Spread) R Package

Language: R - Size: 55.5 MB - Last synced at: 6 days ago - Pushed at: 23 days ago - Stars: 10 - Forks: 5

nextstrain/mpox

Nextstrain build for mpox virus

Language: Python - Size: 34.1 MB - Last synced at: 4 days ago - Pushed at: 5 days ago - Stars: 46 - Forks: 20

nextstrain/forecasts-ncov

SARS-CoV-2 variant growth rates and frequency forecasts

Language: Python - Size: 2.24 MB - Last synced at: 17 days ago - Pushed at: about 1 month ago - Stars: 7 - Forks: 2

sanger-pathogens/snp-sites

Finds SNP sites from a multi-FASTA alignment file

Language: C - Size: 14.7 MB - Last synced at: 22 days ago - Pushed at: over 4 years ago - Stars: 257 - Forks: 49

nextstrain/lassa

Nextstrain build for Lassa virus

Language: Python - Size: 411 KB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 0 - Forks: 5

p-salazarhamm/Picante

Pathogen Informatics Center: Analysis, Networking, Translation & Education

Language: Shell - Size: 85.9 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

sanger-pathogens/iva

de novo virus assembler of Illumina paired reads

Language: Python - Size: 8.46 MB - Last synced at: 4 days ago - Pushed at: almost 4 years ago - Stars: 55 - Forks: 18

sanger-pathogens/mlst_check

Multilocus sequence typing by blast using the schemes from PubMLST

Language: Perl - Size: 5.23 MB - Last synced at: 1 day ago - Pushed at: almost 3 years ago - Stars: 30 - Forks: 15

WCSCourses/AMR_2025 Fork of WCSCourses/AMR_Bacterial_Pathogens

Learn antimicrobial susceptibility testing techniques and how whole-genome sequencing and bioinformatics can be used to understand AMR

Language: HTML - Size: 307 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 1

nextstrain/nipah

Language: Python - Size: 181 KB - Last synced at: 18 days ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

sanger-pathogens/ariba

Antimicrobial Resistance Identification By Assembly

Language: Python - Size: 12 MB - Last synced at: 12 days ago - Pushed at: over 1 year ago - Stars: 173 - Forks: 55

cidgoh/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.

Size: 252 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 9 - Forks: 0

nextstrain/rabies

Language: Python - Size: 151 KB - Last synced at: 18 days ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

szorfein/darkest-space

Minimal colorscheme for vim.

Language: Vim script - Size: 4.7 MB - Last synced at: 16 days ago - Pushed at: over 5 years ago - Stars: 19 - Forks: 1

EliverLara/Antrax

:skull: CLI tool for updating vim pathogen stuff.

Language: JavaScript - Size: 43 KB - Last synced at: 19 days ago - Pushed at: over 7 years ago - Stars: 8 - Forks: 3

nextstrain/oropouche

Oropouche Nextstrain build

Language: Python - Size: 270 KB - Last synced at: 18 days ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

Pathogen-Genomics-Cymru/lodestone

Mycobacterial pipeline

Language: Python - Size: 572 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 11 - Forks: 4

ncsu-landscape-dynamics/pops-core

PoPS Core: C++ library for the Pest or Pathogen Spread Model

Language: C++ - Size: 6.43 MB - Last synced at: 12 days ago - Pushed at: 4 months ago - Stars: 6 - Forks: 2

kwakwaversal/vimfiles

My ~/.vim directory. All hail vim.

Language: Vim Script - Size: 152 KB - Last synced at: about 2 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 0

sanger-pathogens/saffrontree

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Language: Python - Size: 1.32 MB - Last synced at: 1 day ago - Pushed at: almost 5 years ago - Stars: 25 - Forks: 3

sanger-pathogens/Fastaq

Python3 scripts to manipulate FASTA and FASTQ files

Language: Python - Size: 370 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 70 - Forks: 21

quadram-institute-bioscience/albatradis

Comparative TraDIS analysis

Language: Gnuplot - Size: 19.6 MB - Last synced at: about 1 month ago - Pushed at: over 2 years ago - Stars: 9 - Forks: 4

uel3/nf-UnO

metagenomics pipeline supporting The UnO Project for identifying pathogens in common across outbreak samples

Language: Nextflow - Size: 59.8 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 0

nextstrain/avian-flu

Nextstrain build for avian influenza viruses

Language: Python - Size: 2.87 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 19 - Forks: 7

ccdmb/catastrophy

CATAStrophy predicts filamentous plant pathogen lifestyle characteristics based on their CAZyme composition.

Language: Python - Size: 2.08 MB - Last synced at: 7 months ago - Pushed at: over 2 years ago - Stars: 6 - Forks: 0

nextstrain/seasonal-cov

Nextstrain build for seasonal coronaviruses

Language: Python - Size: 2.4 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 1 - Forks: 0

andrewjpage/tiptoft

Predict plasmids from uncorrected long read data

Language: Python - Size: 37.8 MB - Last synced at: 2 days ago - Pushed at: over 5 years ago - Stars: 39 - Forks: 10

evolarjun/stxtyper

STX operon typing

Language: C++ - Size: 722 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 4 - Forks: 1

sanger-pathogens/seroba

k-mer based Pipeline to identify the Serotype from Illumina NGS reads

Language: Python - Size: 19.4 MB - Last synced at: 9 months ago - Pushed at: almost 2 years ago - Stars: 18 - Forks: 16

cidgoh/CanCOGeN_Contextual_Data_Specification

A data specification for harmonizing One Health Canadian COVID pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via a the DataHarmonizer, supported by field and reference guides as well as different curation and new term request SOPs.

Size: 3.16 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

tgolubch/castanet

Data processing scripts for analysis of targeted metagenomics sequencing data. Intended for use with multiplexed Illumina short-read data generated after enrichment.

Language: Python - Size: 27.3 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 2 - Forks: 1

MosaeSat/Livestreams

An open-source project to create a centralized hub for live streaming content.

Language: HTML - Size: 62.5 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

draeger-lab/C_striatum_GEMs

This repository contains all changes made to the strain specific models of Corynebacterium striatum.

Language: HTML - Size: 68.9 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0

solebox/.vim

Language: Vim script - Size: 66.4 KB - Last synced at: 12 months ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0

indexofire/pathongs

Pathogen NGS Documentary

Size: 16.8 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 119 - Forks: 87

indexofire/pangs

Pathogen NGS Documents

Language: HTML - Size: 789 KB - Last synced at: about 1 year ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0

vbrover/stxtyper

STX gene typing

Language: C++ - Size: 719 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 1

chgibb/PHAT

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

Language: TypeScript - Size: 649 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 17 - Forks: 2

selectnull/vimanage

Vim pathogen plugin manager

Language: Shell - Size: 5.86 KB - Last synced at: 5 days ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 0

akshayparopkari/discover_tfbs

Discover transcription factor (TF) binding specificities/sites (TFBS) using binding site motif sequence and structural information.

Language: Python - Size: 177 KB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

sanger-pathogens/Bio-Tradis

A set of tools to analyse the output from TraDIS analyses

Language: Perl - Size: 192 MB - Last synced at: 10 months ago - Pushed at: over 1 year ago - Stars: 20 - Forks: 29

indexofire/bac-ngs-book

病原微生物高通量测序数据分析笔记

Size: 7.68 MB - Last synced at: about 1 year ago - Pushed at: about 6 years ago - Stars: 24 - Forks: 29

sanger-pathogens/gff3toembl

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

Language: Python - Size: 2.92 MB - Last synced at: 1 day ago - Pushed at: over 6 years ago - Stars: 29 - Forks: 12

sanger-pathogens/Artemis

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

Language: Java - Size: 153 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 208 - Forks: 73

sanger-pathogens/plasmidtron

Assembling the cause of phenotypes and genotypes from NGS data

Language: Python - Size: 825 KB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 28 - Forks: 8

sanger-pathogens/assembly-stats

Get assembly statistics from FASTA and FASTQ files

Language: C++ - Size: 1.02 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 95 - Forks: 22

Host-pathogen-evol/Genome-Size-Evolution-Project

HOME OF THE 2-SPEED GENOME MODEL

Language: Jupyter Notebook - Size: 27.7 MB - Last synced at: about 1 year ago - Pushed at: about 8 years ago - Stars: 2 - Forks: 2

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.

Size: 37.1 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 3

sanger-pathogens/pathogen-informatics-training

Language: Jupyter Notebook - Size: 359 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 58 - Forks: 34

ChongLC/MinimalSetofViralPeptidome-UNIQmin

An alignment-independent tool for the study of pathogen sequence diversity

Language: Python - Size: 115 MB - Last synced at: 18 days ago - Pushed at: almost 2 years ago - Stars: 6 - Forks: 3

dazjones/vim-setup 📦

A simple set up script for vim

Language: Vim script - Size: 5.86 KB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

sielerjm/ZF-Diet_Infection

Code used for analysis in the publication: Disentangling the link between zebrafish diet, gut microbiome succession, and Mycobacterium chelonae infection.

Language: HTML - Size: 224 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

bio-ontology-research-group/hpi-predict

The scripts to reproduce the analysis of the HPI prediction paper

Language: Jupyter Notebook - Size: 3.54 MB - Last synced at: about 1 year ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

sanger-pathogens/assembly_improvement

Improve the quality of a denovo assembly by scaffolding and gap filling

Language: Perl - Size: 3.03 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 52 - Forks: 21

Provizanta/ansible-role-vim

Ansible role to install and configure vim along with plugins

Size: 46.9 KB - Last synced at: 12 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

kaworu/vim-coccinelle

pathogen friendly vim syntax files for coccinelle

Size: 105 KB - Last synced at: about 1 month ago - Pushed at: over 11 years ago - Stars: 2 - Forks: 0

ek9/vimrc 📦

NOT MAINTAINED - Code moved to ek9/vim-config

Language: Vim script - Size: 11.7 KB - Last synced at: about 1 month ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 0

Shylock-Hg/viman 📦

Plugin manager of vim.

Language: Python - Size: 112 KB - Last synced at: about 1 month ago - Pushed at: about 6 years ago - Stars: 3 - Forks: 0

jchristi/dotvim

Collection of useful vim plugins via Pathogen and git submodules

Language: Vim Script - Size: 27.3 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

NewLunarFire/wla-vim

WLA Assembly (6502, 65C02, 65816) syntax highlighting

Language: Vim script - Size: 2.93 KB - Last synced at: about 2 years ago - Pushed at: about 8 years ago - Stars: 6 - Forks: 2

nicholaswunz/chytrid-meta-analysis

Paper - Functional disruption varies with infection intensity in an amphibian fungal panzootic

Language: HTML - Size: 8.02 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

rachelambda/hex.vim

A simple vim plugin for hex editing in vim

Language: Vim script - Size: 12.7 KB - Last synced at: 5 days ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 0

havron/dotfiles

:zap: my default environment settings/config

Language: Perl - Size: 419 KB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

BNHM/AmphibiaWebDiseasePortal Fork of jdeck88/AmphibiaWebDiseasePortal

Amphibian Disease Portal 2.0

Language: CSS - Size: 5.88 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

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.

Language: Vim script - Size: 85.9 KB - Last synced at: 19 days ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

SacBase/vim-sac

VIM Pathogen-compatible bundle for highlighting the SaC programming language

Language: Vim script - Size: 8.79 KB - Last synced at: 6 days ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 0

slime-lang/vim-slime-syntax

Language: Vim script - Size: 28.3 KB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 6 - Forks: 5

stefanoschrs/vim

Vim Configuration

Language: Vim script - Size: 33.2 KB - Last synced at: about 1 month ago - Pushed at: about 7 years ago - Stars: 1 - Forks: 0

vaofford/Bio-Deago

Language: HTML - Size: 23 MB - Last synced at: almost 2 years ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 1

runningt/dotfiles

My personal dotfiles. I heve created it to remember my settings, especially vim settings.

Language: Python - Size: 25.4 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

ldmcdaniel/dotfiles

My dotfiles Installation with Interactive Menu

Language: Shell - Size: 423 KB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 5 - Forks: 1

laxman-singh/my-dot-files

This repository contains my custom Dot files(like .vimrc, .zshrc. .bashrc etc).

Language: Shell - Size: 2.93 KB - Last synced at: almost 2 years ago - Pushed at: about 6 years ago - Stars: 1 - Forks: 0

purwnt/vim-workspace

Vim workspace editor for highly configurable text editor for efficiently creating and changing any kind of text. It is included as "vi" with most UNIX systems and with Apple OS X.

Language: Vim script - Size: 9.77 KB - Last synced at: about 21 hours ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

ncsu-landscape-dynamics/PoPSS-R-Legacy

PoPSS (Pest or Pathogen Spread Simulation)

Language: R - Size: 177 MB - Last synced at: about 2 years ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 1

DanielGGordon/dotfiles

They're dotfiles

Language: AutoHotkey - Size: 57.6 KB - Last synced at: about 2 years ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 0

tateg/thelayout

Layouts for Vim, Bash and more!

Language: Ruby - Size: 80.1 KB - Last synced at: about 2 years ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 0