metagenomic-analysis

There are 88 repositories under metagenomic-analysis topic.

  • ggpicrust2

    cafferychen777/ggpicrust2

    Make Picrust2 Output Analysis and Visualization Easier

    Language:R110210513

  • katerinakazantseva/strainy

    Graph-based assembly phasing

    Language:Python665305

  • muellan/metacache

    memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

    Language:C++5774311

  • vmikk/metagMisc

    Miscellaneous functions for metagenomic analysis.

    Language:R4633211

  • MG-RAST/MG-RAST

    The MG-RAST Backend -- the API server

    Language:Perl45111228

  • KennthShang/PhaBOX

    Local version of the virus identification and analysis web server (tool set)

    Language:Python373235

  • cafferychen777/MicrobiomeStat

    Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat

    Language:R322545

  • anuradhawick/LRBinner

    LRBinner is a long-read binning tool published in WABI 2021 proceedings and AMB.

    Language:Python304245

  • ctmrbio/stag-mwc

    StaG Metagenomic Workflow Collaboration

    Language:Python28611413

  • GreyGuoweiChen/VirBot

    VirBot: a protein-based RNA virus detector for metagenomic data

    Language:Python282125

  • MG-RAST/pipeline

    The MG-RAST pipeline

    Language:Common Workflow Language2411319

  • EBI-Metagenomics/pipeline-v5

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

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  • SchulzLab/ORNA

    Fast in-silico normalization algorithm for NGS data

    Language:C++224144

  • treangenlab/lemur

    Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets

    Language:Python22341

  • Ivarz/Conifer

    Calculate confidence scores from Kraken2 output

    Language:C21297

  • pnnl/mercat

    MerCat: python code for versatile k-mer counting and diversity estimation for database independent property analysis for meta -ome data

    Language:Python186011

  • anuradhawick/seq2vec

    Fast sequence vectorization for metagenomics analysis. Converts input sequences into oligonucleotide frequency vectors, fast!

    Language:C++14540

  • tmbuza/iMAP

    iMAP v1.0 (Pre-release): Integrated Microbiome Analysis Pipeline

    Language:HTML13214

  • CMU-SAFARI/Genome-on-Diet

    Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version: https://arxiv.org/abs/2211.08157).

    Language:Roff11714

  • mmpust/raspir

    Raspir, the rare species identifier

    Language:Python112153

  • raw-lab/mercat2

    MerCat2: python code for versatile k-mer counting and diversity estimation for database independent property analysis for metaome data

    Language:HTML114101

  • snz20/carnelian

    Language:Python11161

  • 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

    Language:Python9131

  • sipost1/kraken2OTUtable

    Creates a simple OTU table from Kraken2 report.

    Language:Python8121

  • 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 Notebook7402

  • pjtorres/metagenomics_tutorial

    Analyzing shotgun data

    Language:HTML6112

  • pfeiferd/genestrip

    Genestrip - Efficient read classification, filtering and k-mer counting for selected groups of species

    Language:Java5100

  • QuentinLetourneur/Let-it-bin

    Optimize workflow for binning metagenomic short reads from multiple samples

    Language:Nextflow5302

  • rusher321/rmeta

    collect the R function for daily work

    Language:HTML5232

  • 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++5210

  • 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.

    4202

  • CMU-SAFARI/MetaTrinity

    MetaTrinity is a novel metagenomic analysis tool employing efficient containment search techniques and heuristics for read mapping to achieve significant speedup while maintaining high accuracy. This positions MetaTrinity as an efficient solution, optimally balancing speed and precision in metagenomic analysis.

    Language:HTML4511

  • MattCzajkowski/GenCoF

    A graphical user interface for a genomic contamination filtering pipeline to filter out reads from metagenomic files

    Language:C++4404

  • bo1929/CONSULT-II

    Accurate taxonomic classification and abundance profiling using locality-sensitive hashing.

    Language:C++3010
  • Geomosaic

    giovannellilab/Geomosaic

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

    Language:Python3601

  • ZiyueYang01/Phyrvm

    Phyrvm: A one-stop software solution for RNA virus mining and host-association prediction

    Language:Python3100