Anyi Hu's repositories
qcmi
To explore ecological associations of microbial communities
METABOLIC
A scalable high-throughput metabolic and biogeochemical functional trait profiler
CompRanking_Taxonomy_Tutorial
An tutorial for arg_ranker and tell the users how to gain the desired result step by step.
BioSAK
A Swiss-Army-Knife for Bioinformaticians
ARGminer
Curation of Antibiotic Resistance Genes by using crowdsourcing
MMseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
EasyMicroPlot
R package for downstream Microbiome analysis
aviary
A hybrid assembly and MAG recovery pipeline (and more!)
GTDBTk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
mOTUs
motus - a tool for marker gene-based OTU (mOTU) profiling
kingfisher-download
Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.
phamb
Downstream processing of VAMB binning for Viral Elucidation
vamb
Variational autoencoder for metagenomic binning
graftM
GraftM - Rapid community profiles from metagenomes
MGEfams
Fast and robust identificaiton of mobile genetic elements (MGE) genes from genomes and metagenome assemblies using MGEfams, a high-quality and manually cruated subdatabase of profile hidden Markov models for MGE genes
phylophlan
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
enrichM
Toolbox for comparative genomics of MAGs
rush
A cross-platform command-line tool for executing jobs in parallel
bioinformatics-snakemake-pipelines
Collection of Snakemake pipeline for commin bioinformatics tasks
pyani
Application and Python module for average nucleotide identity analyses of microbes.
seqtk
Toolkit for processing sequences in FASTA/Q formats