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abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

awesome

Awesome resources on Bioinformatics, data science, machine learning, programming language (Python, Golang, R, Perl) and miscellaneous stuff.

awesome-chatgpt-prompts-zh

ChatGPT 中文调教指南。各种场景使用指南。学习怎么让它听你的话。

bac-genomics-scripts

Collection of scripts for bacterial genomics

chewbbaca

BSR-Based Allele Calling Algorithm

chicken-pangenome-paper

Scripts used to perform analyses in Rice et al. (2023)

clin-mngs

Clin-mNGS: Automated pipeline for pathogen detection from clinical metagenomic data

cobra_analysis

cobrapy

COBRApy is a package for constraint-based modeling of biological networks

codon-usage

Analyse Codon Usage in E.coli and S.solfataricus

codonpy

cvn001.github.io

Hexo Blog

datasets

Benchmark datasets for WGS analysis

deeplearning-biology

A list of deep learning implementations in biology

dimensionreduction

Shiny app for dimension reduction using UMAP and t-SNE

dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow

easymicrobiome

Scripts and databases for amplicon and metagenome

eggnog-mapper

enterobasegenomeassemblydownload

Python script for downloading assemblies from enterobase

ggplot2-china-map

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

gitskills

go_kegg_annotation

GO KEGG annotation

haphpipe

NGS viral assembly and population genetics

hiv-drives

hiv-drm-machine-learning

This repo contains the data and software used to run the analyses in the "Using machine learning and Big data to explore the drug resistance landscape in HIV"

hivepisimanalysis

hivmmer

Alignment and variant-calling pipeline for Illumina HIV sequences.

kraken2

The second version of the Kraken taxonomic sequence classification system

kvasir

Searching for Horizontal Gene Transfer

learngit