Anyi Hu's repositories
ARG-contig_mobilome_analysis
This pipeline performs a mobilome analyses on previously selected contigs
ARGfams
Fast and robust identificaiton of antibiotic resistance genes (ARGs) from microbial genomes and metagenome assemblies using ARGfams, a high-quality and manually cruated subdatabase of profile hidden Markov models for ARGs
args_oap
ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes Detection from Metagenomic Data Using an Integrated Structured ARG Database
biobakery
bioBakery tools for meta'omic profiling
bit
Bioinformatics Tools
cariaco_basin
Scripts for analyses of particle-associated and free-living metagenomic and metatranscriptomic datasets from the permanently anoxic water column of the Cariaco Basin, Venezuela as part of the CARIACO Ocean Time Series project.
CoverM
Read coverage calculator for metagenomics
deepTools
Tools to process and analyze deep sequencing data.
DRAM
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
EdwardsLab
Code from the Edwards lab, including bioinformatics, image analysis and more. All this code is created and maintained by folks at Rob Edwards' bioinformatics lab at Flinders University
fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
genomad
geNomad: Identification of mobile genetic elements
gggenomes
A grammar of graphics for comparative genomics
GToTree
A user-friendly workflow for phylogenomics
gut_resistome-useful
This is for manuscript of study about resistome in human and food animal gut.
iMetaPlot
iMeta teaches you to plot
metapi
A general metagenomics data mining system focus on robust microbiome research
mfqe
FASTA/FASTQ extractor for multiple sets of read names
Mito-COI
Mito-COI database
mobileOG-db
code repo for mobileOG-db
Phosphorus-cycling-database
This is a comprehensive database for fast and accurately analyzing the phosphorus cycling database.
salmon
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
singlem
De-novo OTUs from shotgun metagenomes
TBtools
GUI/CommandLine Tool Box for biologistists to utilize NGS data.
VirusTaxo_Hierarchical
Implementation of https://doi.org/10.1016/j.ygeno.2022.110414
What_the_Phage
WtP: Phage identification via nextflow and docker or singularity