Mark Renton (indexofire)

indexofire

Geek Repo

Company:HZCDC

Location:Zhejiang, Hangzhou

Home Page:https://indexofire.github.io/pathongs/

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Mark Renton's starred repositories

PhyloTrace

PhyloTrace is a GUI platform for a fully controllable cgMLST analysis workflow.

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pca-book

Source files for a book on Principal component analysis

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public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.

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awesome-genome-visualization

A list of interesting genome browser or genome-browser-like implementations

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SyntenyFinder

SyntenyFinder contains a collection of scripts to easily perform and visualize macrosynteny analysis when provided with the accessions of annotated chromosome-level genome assemblies from NCBI.

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VPsero

rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes

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AllTheBacteria

Follow up to Grace Blackwell's 661k dataset, for 2023

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ecoli_serotyping

In silico prediction of E. coli serotype

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vista

The Pathogenwatch Vibrio cholerae genotyping tool

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ComfyUI

The most powerful and modular stable diffusion GUI, api and backend with a graph/nodes interface.

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Grandeur

UPHL's Reference Free Pipeline

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awk-hack-the-planet

Source code repo for Ben Porter (FreedomBen)'s free course on Awk (originally a talk at Linux Fest Northwest 2019 and 2020)

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assembly_accuracy

tools for assessing the accuracy of genome assemblies

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fujiplot

:mount_fuji: Fuji plot—a circos representation of multiple GWAS results— :mount_fuji:

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genomad

geNomad: Identification of mobile genetic elements

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dnaapler

Reorients assembled microbial sequences

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MetaPhlAn

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

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rerio

Research release basecalling models and configurations

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dragonflye

:dragon: :fly: Assemble bacterial isolate genomes from Nanopore reads

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pairsnp

A set of scripts for calculating pairwise SNP distance

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gravis

Interactive graph visualizations with Python and HTML/CSS/JS.

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genomics_adventure

Workshop on Genomics - Genomics Adventure

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awesome-nanopore

A curated list of awesome nanopore analysis tools.

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appwrite

Your backend, minus the hassle.

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ExpansionHunterDenovo

A suite of tools for detecting expansions of short tandem repeats

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ShigaPass

An in silico tool to predict Shigella serotypes

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nfvibrio

Nextflow pipeline to run metagenomic sequence analysis of Vibrio Parahaemolyticus, based on nf-core template, by John Palmer & Zohaib Anwar

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fastq-dl

Download FASTQ files from SRA or ENA repositories.

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