pathogen

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

Pathogen NGS Documentary

Get assembly statistics from FASTA and FASTQ files

Python3 scripts to manipulate FASTA and FASTQ files

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

de novo virus assembler of Illumina paired reads

Assembling the cause of phenotypes and genotypes from NGS data

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

Predict plasmids from uncorrected long read data

Multilocus sequence typing by blast using the schemes from PubMLST

病原微生物高通量测序数据分析笔记

Minimal colorscheme for vim.

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

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

A set of tools to analyse the output from TraDIS analyses

Comparative TraDIS analysis

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

The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted 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. The Pathogen Transmission Ontology is available under CC0 license (https://creativecommons.org/publicdomain/zero/1.0/).

💀 CLI tool for updating vim pathogen stuff.

PoPS (Pest or Pathogen Spread) R Package

My dotfiles Installation with Interactive Menu

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

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