metagenomic-pipeline
There are 2 repositories under metagenomic-pipeline topic.
- metaTORLanguage:Python 22
EBI-Metagenomics / pipeline-v5
This repository contains all CWL descriptions of the MGnify pipeline version 5.0.
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new-atlantis-labs / Metagenomics
🐋 The Living Oceans Metagenome Taxanomic Profiling tool (beta) is a metagenomic pipeine built to work on your local ocean
Language:Jupyter Notebook 7zaidissa / MetaRon
Metagenomic opeRon Prediction pipeline. MetaRon presents the first pipeline for the prediction of metagenomic operons without any functional or experimental data.
Language:Python 7Finesim97 / MetaErgInstallHelper
A few scripts to help with the installation of MetaErg, the contig/bin annotation pipeline
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treangenlab / komb
KOMB is a tool for fast identification of unitigs of interest in metagenomes. KOMB introduces the concept of a Hybrid Unitig Graph (an extension to compacted de Bruijn graphs) and relies on k-core and K-truss decomposition algorithms.
Language:C++ 5ac1513 / MAGqual
MAGqual is a command line tool to evaluate the quality of metagenomic bins and generate recommended metadata in line with the MIMAG standards
Language:Python 4Brochado-Kith / microbiome_analysis
The following codes are focused on microbiome analysis, alpha, beta and relative abundance differences.
Language:R 3cafferychen777 / MicrobiomeStat-Turtorial-Professional-Version
MicrobiomeStat Tutorial Repository: This is a comprehensive resource for learning how to use the MicrobiomeStat package. It provides a step-by-step guide to effectively analyze complex microbiome data.
- Geomosaic
giovannellilab / Geomosaic
A flexible metagenomic pipeline combining read-based, assemblies and MAGs with downstream analysis
Language:Python 3 hivlab / quantify-virome
quantify-virome: identify and quantify viruses from metagenomic shotgun sequences
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balazshorvathreal / MegaVir
MegaVir is a bioinformatic pipeline for virome characterization and genome assembly.
Language:R 1bioinfonupeb / microbiota_da_mulher_lbbm
Projeto de análise metagenômica e metabolômica da microbiota de mulheres no climatério - LBBM UFOP
Language:HTML 1Metagenomic analysis of the project: "PROGRAMAÇÃO METABÓLICA INDUZIDA PELA SUPERLACTAÇÃO E SEUS EFEITOS NA ATIVAÇÃO DO INFLAMASSOMA NLRP3 E EXPRESSÃO DO MIR-155 EM MODELO EXPERIMENTAL DE RESISTÊNCIA À INSULINA"
Language:Jupyter Notebook 1BioSina / MAPle
MAPle provides three different modules for the analysis of paired-end short read metagenomic data
Language:Python 1jimmlucas / wgs-metasociomic
WGS- Metasociomic- analysing bacterial social interactions in metagenomes of longitudinally collected samples of human microbiomes
Language:Nextflow 1lauralwd / Azolla_genus_metagenome
This project aims do describe and explore the metagenomes of fern species of the genus Azolla.
Language:Python 1NerdVerse2024 / Milk_metagenomics
Milk Metagenomics Analysis of Cow Milk Samples across Global sites Using Mothur
Nimauric / Mapler
A metagenome assembly and evaluation pipeline, focused on hi-fi long reads, but with support for lo-fi long reads and hybrid assemblies
Language:Python 1Ahmed-A-Mohamed / metaGEENOME
metaGEENOME is a 16S rRNA metagenomic analysis tool that encompasses nearly all steps of downstream analysis.
Language:R 0EXPOSIÇÃO AGUDA AO CHUMBO E SUA RELAÇÃO COM ALTERAÇÕES NO STATUS REDOX E DISBIOSE INTESTINAL EM RATOS
Language:Jupyter Notebook 0hermidalc / dragonfish
A fast, efficient, and accurate functional and taxonomic meta-omic profiler built on Pufferfish and the ccdBG
Language:Python 0karamveerverma37 / Silva_output_merger
Silva OTU count table merger
Language:Perl 0LaboratorioBioinformatica / MAGset
MAGset is a tool to analyze and compare MAGs of known species
Language:Java 0VictorCalderon / megazor-metagenomics
A pipeline for metagenomic analysis
Language:Shell 0huyvanvnese / Metagenomics-Analysis-on-NIG-Supercomputer
Simple Script for Metagenomics Analysis on NIG Supercomputer (National Institute of Genetics)
Nirmal2310 / MetaSutra
This pipeline takes the raw metagenomic WGS reads as an input, assemble them, separate the contigs in MAGs, taxonomically classify the MAGs and quantify the ARGs in the MAGs. The pipeline is built using R Shiny and people can run end to end analysis by doing few clicks on the screen.
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