metagenomic-pipeline

There are 2 repositories under metagenomic-pipeline topic.

• metaTOR

  koszullab / metaTOR

  Metagenomic binning based on Hi-C data

  metagenomicshi-c3cmetagenomic-pipelinemetagenome-assemblylouvain-community-detection
  Language:Python 26

• EBI-Metagenomics / pipeline-v5

  This repository contains all CWL descriptions of the MGnify pipeline version 5.0.

  common-workflow-languagecwlworkflowcwl-descriptionscwl-workflowmgnifymetagenomic-pipelinemetagenomic-analysismetagenomic-classificationmetagenomic-datametagenomicsamplicon-pipelinewgs-analysis
  Language:HTML 23

• frubino / mgkit

  MGKit: Metagenomics Framework

  bioinformaticsmetagenomicsmetagenomic-pipelinemicrobiology
  Language:Python 16

• ac1513 / MAGqual

  MAGqual is a command line tool to evaluate the quality of metagenomic bins and generate recommended metadata in line with the MIMAG standards

  metagenomic-analysismetagenomic-pipelinemetagenomicssnakemakesnakemake-pipeline
  Language:Python 14

• ukhsa-collaboration / LOMA

  A Nextflow pipeline designed to classify, align and assemble nanopore metagenomic reads.

  metagenomic-pipelineoxford-nanopore-sequencing
  Language:Nextflow 13

• new-atlantis-labs / Metagenomics

  🐋 The Living Oceans Metagenome Taxanomic Profiling tool (beta) is a metagenomic pipeine built to work on your local ocean

  bioinformaticsbioinformatics-pipelinepythonpython3metagenomic-analysismetagenomic-pipelinemetagenomicsplanktongitcoinoceandescigitcoin-grantsresci
  Language:Jupyter Notebook 8

• zaidissa / MetaRon

  Metagenomic opeRon Prediction pipeline. MetaRon presents the first pipeline for the prediction of metagenomic operons without any functional or experimental data.

  metagenomicsmetagenomic-operonsmetagenomic-pipelinemetagenomic-data-processing
  Language:Python 7

• cafferychen777 / 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.

  16s16s-rrna16s-seqanalysisdata-analysismetagenomesmetagenomic-analysismetagenomic-pipelinemetagenomicsmicrobiomemicrobiome-analysismicrobiome-analysis-pipelinesmicrobiome-datamicrobiome-workflowomicsomics-dataomics-data-analysisomics-data-integrationvisualization
  6

• rcs333 / CLOMP

  :horse: CLinically Okay Metagenomic Pipeline :horse:

  metagenomicsmetagenomic-classificationmetagenomic-datametagenomic-pipelinetaxonomysequencingnext-generation-sequencingngs-pipeline
  Language:Python 6

• 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.

  anomaly-detectionk-core-decompositionmetagenomic-analysismetagenomic-pipelinemetagenomicsshort-read-sequencing
  Language:C++ 6

• Finesim97 / MetaErgInstallHelper

  A few scripts to help with the installation of MetaErg, the contig/bin annotation pipeline

  metagenomic-pipelinemetagenomesannotation
  Language:Shell 5
• Geomosaic

  giovannellilab / Geomosaic

  A flexible metagenomic pipeline combining read-based, assemblies and MAGs with downstream analysis

  metagenomicsmicrobial-communitiesmetagenomic-analysismetagenomic-pipelinepipelinewgswhole-genome-sequencingcustomizable
  Language:Python 4

• Brochado-Kith / microbiome_analysis

  The following codes are focused on microbiome analysis, alpha, beta and relative abundance differences.

  16salpha-diversitybeta-diversitymicrobiomemicrobiome-analysismicrobiome-workflowphyloseqrstudioshinnybetadiversitymetagenomic-pipeline
  Language:R 3

• hivlab / quantify-virome

  quantify-virome: identify and quantify viruses from metagenomic shotgun sequences

  snakemake-workflowsviromemetagenomicsmetagenomic-pipelinesnakemakevirome-workflowtaxonomy
  Language:Python 3

• muneebdev7 / metabolt

  MetaBolt: Lightning fast & automated metagenomic pipeline powered by Nextflow

  metagenome-assemblymetagenome-binningnextflownf-coremetagenomic-analysismetagenomic-pipeline
  Language:Nextflow 3

• avishekdutta14 / iMAGine

  iMAGine - In silico Metagenomics Pipeline

  metagenomic-pipeline
  Language:Python 2

• bioinfonupeb / redemicro-ana-flavia-nutri

  Metagenomic 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"

  bioinformaticsmetagenomic-pipelinemetagenomicspythonqiime2
  Language:Jupyter Notebook 2

• QIngyuanfl / predict-annotation-for-metagenome

  宏基因组预测

  metagenomic-pipeline
  Language:Python 2

• balazshorvathreal / MegaVir

  MegaVir is a bioinformatic pipeline for virome characterization and genome assembly.

  amino-acidsbacteriaeukaryotesmetagenomic-pipelinenucleotidesvirus
  Language:R 1

• bioinfonupeb / microbiota_da_mulher_lbbm

  Projeto de análise metagenômica e metabolômica da microbiota de mulheres no climatério - LBBM UFOP

  shell-scriptmetagenomic-pipelinemetagenomic-analysisqiime2metabolomicsbioinformatics-pipeline
  Language:HTML 1

• BioSina / MAPle

  MAPle provides three different modules for the analysis of paired-end short read metagenomic data

  bioinformaticsbioinformatics-analysisbioinformatics-pipelinebioinformatics-toolmetagenomic-analysismetagenomic-pipelinemetagenomicsmicrobiomemicrobiome-analysispythonpython-script
  Language:Python 1

• jimmlucas / wgs-metasociomic

  WGS- Metasociomic- analysing bacterial social interactions in metagenomes of longitudinally collected samples of human microbiomes

  bacterial-genome-analysismetagenomic-analysismetagenomic-pipelinemetasociomic
  Language:Nextflow 1

• lauralwd / Azolla_genus_metagenome

  This project aims do describe and explore the metagenomes of fern species of the genus Azolla.

  azollasymbiosismetagenomesplantmetagenomicsmetagenomic-pipelinemetagenome-assemblysnakemakecondabiocondabioinformaticsbioinformatics-pipelinebiological-data-analysisfair-dataendophytessymbiont
  Language:Python 1

• NerdVerse2024 / Milk_metagenomics

  Milk Metagenomics Analysis of Cow Milk Samples across Global sites Using Mothur

  data-analysismetagenomic-pipelinemicrobiomemothurrna-seq
  1

• PopovIILab / KrakenParser

  🗂️Parse multiple Kraken2 reports into CSV files on 6 taxonomical levels

  kraken2krakentoolsmetagenomic-pipelinemetagenomics
  Language:Shell 1

• Ahmed-A-Mohamed / metaGEENOME

  metaGEENOME is a 16S rRNA metagenomic analysis tool that encompasses nearly all steps of downstream analysis.

  16srrnaalpha-diversitybeta-diversitymetagenomic-analysismetagenomic-pipelinestatistical-analysis
  Language:R 0

• bioinfonupeb / redemicro-miliane-nutri

  EXPOSIÇÃO AGUDA AO CHUMBO E SUA RELAÇÃO COM ALTERAÇÕES NO STATUS REDOX E DISBIOSE INTESTINAL EM RATOS

  bioinformaticsmetagenomic-pipelinemetagenomicspythonqiime2
  Language:Jupyter Notebook 0

• bioinfonupeb / redemicro-thayane

  Metagenomic characterization of the intestinal microbiota of postmenopausal Brazilian women.

  bioinformatics-pipelinemetagenomic-analysismetagenomic-pipelinemenopause
  Language:Jupyter Notebook 0

• hermidalc / dragonfish

  A fast, efficient, and accurate functional and taxonomic meta-omic profiler built on Pufferfish and the ccdBG

  metagenomicsfunctional-profilingmetagenomic-analysismetagenomic-pipelinemetatranscriptomic-analysismetatranscriptomic-pipelinemetatranscriptomicstaxonomic-classificationtaxonomic-profilingmicrobiome-analysismicrobiome-workflow
  Language:Python 0

• huyvanvnese / Metagenomics-Analysis-on-NIG-Supercomputer

  Simple Script for Metagenomics Analysis on NIG Supercomputer (National Institute of Genetics)

  bioinformatics-pipelinemetagenomic-analysismetagenomic-pipeline
  0

• karamveerverma37 / Silva_output_merger

  Silva OTU count table merger

  consolidationfunctional-profilingmetagenomic-pipelinemetagenomicsotu-table
  Language:Perl 0

• 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

  bioinformaticslong-readsmetagenomic-pipeline
  Language:Jupyter Notebook 0

• 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.

  antimicrobial-resistance-genesmetagenomic-pipelineshinyapptaxnomic-classification
  Language:HTML 0

• ruppinlab / tcga-wgs-kraken-microbial-quant

  Kraken2 + Bracken based pipeline for classifying and quantifying microbial reads from GDC TCGA WGS data

  bioinformatics-pipelinebioinformatics-workflowmetagenomic-pipelinemetagenomicsmetagenomics-taxon-profilingsnakemake-pipelinesnakemake-workflow
  Language:Python 0

• VictorCalderon / megazor-metagenomics

  A pipeline for metagenomic analysis

  bioinformaticsbioinformatics-pipelinemetagenomic-pipeline
  Language:Shell 0

• zehrakorkusuz / Microbial_Genomics

  Oral Microbiome & Metagenomic analysis for the Characterization of a uSGB

  metagenomic-analysismetagenomic-pipelinemicrobiome
  Language:Jupyter Notebook 0