cvn001

mamba

The Fast Cross-Platform Package Manager

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

RawTherapee

A powerful cross-platform raw photo processing program

vg

tools for working with genome variation graphs

bactopia

A flexible pipeline for complete analysis of bacterial genomes

pggb

the pangenome graph builder

NGS-analysis

二代测序数据分析

plotsr

Tool to plot synteny and structural rearrangements between genomes

chewBBACA

BSR-Based Allele Calling Algorithm

Ratatosk

Hybrid error correction of long reads using colored de Bruijn graphs

WANIMAL-1983

WANIMAL(王动)全部原版资源免费分享，目前WANIMAL作品在黑市上最高被炒到了5000多元，本项目整理了WANIMAL从2013年到现在的所有作品，建议在电脑查看图片效果会更好（目前更新到2020年3月，共8765张图片，大小16.1G，还会持续更新）

BactDating

Bayesian inference of ancestral dates on bacterial phylogenetic trees

GenoVi

GenoVi, an automated customizable circular genome visualizer for bacteria and archaea

TGG

tomato graph pangenome

NucDiff

In-depth characterization and annotation of differences between two sets of DNA sequences

Lumix-V-log-LUTs

Free LUTs for Panasonic Lumix Vlog color grading

phyloscanner

Phylogenetics between and within hosts at once, all along the genome.

MGCplotter

Microbial Genome Circular plotting tool for comparative genomics using Circos

SeqSero2

SeqSero2

ggplot2-china-map

Use ggplot2 to plot China map, and provide a JSON file of coordinates of major Chinese cities

GO_KEGG_annotation

GO KEGG annotation

VGEA

VGEA (Viral Genomes Easily Analyzed) is a pipeline for analysis of RNA virus next-generation sequencing data.

PopPIPE

Population analysis PIPEline 🛠🧬

codfreq

FASTQ-to-CodFreq pipeline for HIV-1 and SARS-CoV-2

hivmmer

Alignment and variant-calling pipeline for Illumina HIV sequences.

haphpipe

NGS viral assembly and population genetics

GENERA

ccne

Carbapenemase-encoding gene copy number estimator

gnomonicus

Python code to integrate results of tb-pipeline and provide an antibiogram, mutations and variants

Pangenome-Graphs-in-Infectious-Disease

This repository contains simulated datasets and scripts used for the research paper titled "Pangenome Graphs in Infectious Disease: A Promising and Practical Implementation for Comprehensive Genetic Variation Analysis."