A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.

Workflow to calculate ANIr and sequence coverage (depth and breadth) of genome(s) / MAG(s) from metagenomes by gene, intergenic region, contig, and whole genome.

Repository with scripts to normalize relative abundance (TAD/GEQ, RPKM or recruited reads) at a given nonpareil coverage

Fast and accurate Average Genome Size and 16S rRNA gene Average Copy Number computation in metagenomic data

ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.

ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes Detection from Metagenomic Data Using an Integrated Structured ARG Database

This is a small script used to calculate coverage from BWA MEM using samtools, bedtools, and python3

My resume in LaTeX (template suited for new graduates; 应届生简历模板)

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Recovery of prokaryotic genomes from shotgun metagenomic sequencing data

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

Horizontal gene transfer (HGT) identification pipeline

MGnify genome analysis pipeline

A tool to classify sequences of plasmid or chromosomal origin. A paper describing this tool is available at: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007781

Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.

Using R language in microbiome analysis

It includes all the code used in this manuscript

Computer code for the manuscript "Climate Warming Enhances Microbial Network Complexity and Stability"

Antibiotic resistance genes (ARGs) have accelerated microbial threats to human health during the last decade. Here we determined the risk of ARGs from multiple perspectives by using these code.

Scripts and tutorials on how to assemble individual microbial genomes from metagenomes

Virus Identification By iteRative ANnoTation

Scripts to quality control for metagenomic raw data, including removing the adapters, low quality reads, bases or PCR duplicates

Interpretation and visualization of microbiome charts

A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.

This is the source code for multisamples ARGs profiling using SARG2.0 database

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 hidde…

A comprehensive pipeline for short read metagenomic data