alienzj

gtdb2ncbi

GTDB => NCBI

fastcluster

Fast hierarchical clustering routines for R and Python.

abricate

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

alphafold

Open source code for AlphaFold.

anvio

An analysis and visualization platform for 'omics data

ChatGPT

🔮 ChatGPT Desktop Application (Mac, Windows and Linux)

CheckM

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Chinese-Resume-in-Typst

使用 Typst 编写的中文简历, 语法简洁, 样式美观, 开箱即用, 可选是否显示照片

CoverM

Read coverage calculator for metagenomics

DBSCAN-SWA

DEEP-HLA

Upload test

DeepVirFinder

Identifying viruses from metagenomic data by deep learning

doomemacs

An Emacs framework for the stubborn martian hacker

drep

Rapid comparison and dereplication of genomes

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

fastq-dl

Download FASTQ files from SRA or ENA repositories.

GTDBTk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

kneaddata

Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.

kodama

Fast hierarchical agglomerative clustering in Rust.

KrakenTools

KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

Maaslin2

MaAsLin2: Microbiome Multivariate Association with Linear Models

MP_supplementary_file

multitax

Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)

read2tree

a tool for inferring species tree from sequencing reads

skani

Fast, robust ANI and aligned fraction for metagenomic genomes and contigs

TidyMultiqc

Converts 'MultiQC' Reports into Tidy Data Frames

tmux-config

TMwR

Code and content for "Tidy Modeling with R"

tximeta

Transcript Quantification Import with Automatic Metadata

winapps

Run Windows apps such as Microsoft Office/Adobe in Linux (Ubuntu/Fedora) and GNOME/KDE as if they were a part of the native OS, including Nautilus integration.