Shotgun metagenomics pipeline to process microbiome samples
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Updated
Jun 6, 2024 - Shell
Shotgun metagenomics pipeline to process microbiome samples
Reconstruction and analysis of viral and host genomes at multi-organ level
Build scripts for bioinformatics applications used by MGX
Quantitative metagenomic alignment and taxonomic exact-matching
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
plotting metagenomics otu abundances
Scripts used by George S. Long
MetaFX – library for feature extraction from whole-genome metagenome sequencing data
metagenome simulation for targeted and reduced-representation sequencing
viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data
The text files in this repository are tools that I've used during metagenomic assembly including: trimming, quality checking, assembly, dereplication, annotation, and analysis.
Profiler for metagenomics based on NGLess
RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties.
DEPRECATED: Use Cenote-Taker 3 instead
Metagenomic functional annotation pipeline
Arche: a functional-optimized annotator for microbial meta(genomes)
Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data
Qiime 2, an advanced bioinformatics platform, specializes in analyzing metagenomic data. With a modular plugin architecture, integrated workflows, and visualization tools, Qiime 2 facilitates reproducible and transparent analyses, supporting both command-line and GUI interactions.
NGS4ECOPROD - An easy-to-use conda environment and pipelines for metagenome sequence analysis
A collection of NGLess modules open to community contributions
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