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Database of genomes integrated from the gut microbiome and other environments
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Improvement of metagenome-assembled genomes
Code used to generate figures for the MetaSUB Main Paper Released August 2019
Horizontal gene transfer (HGT) identification pipeline
NastyBugs: a simple method for extracting antimicrobial resistance information from metagenomes
Metagenomics course
This repository contains all the scripts used for metagenomic processing and resistome. First, metagenome sequences from cattle feces were analyzed with AmrPlusPlus for sequence processing and ARG annotations with the MEGARES 2.0 database. Then, host-removed metagenomes were used for DNA assembly and further annotations with DeepARG, CARD, and HMD-ARG which are protein databases to identify antimicrobial determinants. Finally, ARG-host identification was carried out by identifying taxa associated with ARG-carrying contigs and co-occurrence networks between bacterial taxa and ARGs. Statistical analyses were used to identify assembler performance and resistome composition.
MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome
MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
Contains a fasta format database of a large variety of mobile genetic elements and an annotation file
Scripts and tutorials on how to assemble individual microbial genomes from metagenomes
Analyze a set of genomes with the anvi'o pangenome pipeline
pb-metagenomics-tools
Plascad is a computationally efficient tool designed for plasmids classification, antibiotic resistance genes (ARGs) annotation and plasmid visualization.
Procedure to annotate antibiotic resistance genes (ARGs) referenced by the CARD database using PROKKA
A toolbox for improving metagenome-assembled genomes.
Copies a list of files from one folder to another
Highly sensitive pathogen detection
Split a big folder into several.
A robust, extensible metagenomics pipeline
Generating iToL annotations from Spreadsheet or CSV files
Target / Integrative Genetic Element Retriever: precisely maps IGEs (a defined type of genomic island) in bacterial and archaeal genomes; package also includes orthogonal program Islander
A set of scripts used for tracking structural variations around a gene of interest
This is the source code for multisamples ARGs profiling using SARG2.0 database
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.