Awesome Open Source

Programming Languages

Search results for metagenomics

276 search results found

Phylogenetic Placement Evaluation Workflows : Benchmark placement software and different reference trees

A pipeline for construction and graphical visualization of annotated pangenome networks.

Py Metagenomics ⭐ 9

Some python libs and scripts for metagenomic analyses

Cosmosid Cli ⭐ 9

Command line client and Python libraries for CosmosID API

Microbiome Informatics - API and service usage examples

Glimmer Mg ⭐ 9

Gene prediction in metagenomic sequences using Glimmer augmented by phylogenetic classification and clustering

Superpang ⭐ 9

Non-redundant pangenome assemblies from multiple genomes or bins

Livermore Metagenomic Analysis Toolkit

Rapid, Alignment-free, Phylogenetic Placement via Ancestral Sequences

Metagenomics Analysis ⭐ 8

Data Processing and Visualization for Metagenomics

Functional Analysis of Metagenomes by Likelihood Inference

MGKit: Metagenomics Framework

Msamtools ⭐ 8

Metagenomics-related extended functionalities to samtools

ViralCC: leveraging metagenomic proximity-ligation to retrieve complete viral genomes

fast classification of metagenomic sequences with lightweight de Bruijin graph-based reference indexing

Notebooks ⭐ 8

MGnify documentation and Jupyter Lab notebooks to support downstream analysis of MGnify data (EMBL-EBI's metagenomics platform)

A simulator for horizontal gene transfer (HGT) in microbial communities

Metacrast ⭐ 8

MetaCRAST: reference-guided CRISPR detection in metagenomes

Shotgun Metagenomics Pipeline ⭐ 8

A pipeline for primary analysis of shotgun metagenomic sequencing data

GDmicro - Use GCN and Deep adaptation network to classify host disease status based on human gut microbiome data.

Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data

[AAAI'22] RepBin: Constraint-Based Graph Representation Learning for Metagenomic Binning

Omixer Rpm ⭐ 7

A Reference Pathways Mapper for turning metagenomic functional profiles into pathway/module profiles.

Metassemble ⭐ 7

Scripts to run several metagenomics assembly programs

Findfungi ⭐ 7

A pipeline for the identification of fungi in public metagenomics datasets

Background depletion/extraction using k-mer and/or alignment methods 🐼

Damage parameter estimation for ancient DNA

Boldigger Commandline ⭐ 7

BOLDigger as a commandline tool

zAMP is a bioinformatic pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics

Strainflye ⭐ 7

Pipeline for analyzing (rare) mutations in metagenome-assembled genomes

Chordomics ⭐ 7

Interactive visualisation and data annotation for meta-omics data

Bettercallsal ⭐ 7

Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.

Omixer Rpmr ⭐ 7

An R interface to the omixer-rpm for turning metagenomic functional profiles into pathway/module profiles

Nanometa_live ⭐ 7

A streamlined workflow and GUI for real-time species identification and pathogen characterization via nanopore sequencing data. Engineered for precision, speed, and user-friendliness, with offline functionality post-initialization.

Fraggenescanplusplus ⭐ 6

Scalable high-throughput short-read open reading frame prediction

K2Mem is a variant of Kraken 2 taxonomic sequence classification system that can learn from the previous classifications.

Lavalampplot ⭐ 6

instructions, python and R code for generating lava lamp plots of kmer coverage

Pathostat ⭐ 6

The purpose of this package is to perform Statistical Analysis on the PathoScope generated reports files.

Environmental_metagenomics ⭐ 6

A quick workflow to get researchers started with the bioinformatic pipeline used in the Environmental Metagenomics program.

Tofu Maapo ⭐ 6

Nextflow pipeline for the analysis of metagenomic short reads.

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

MGLEX – A Python Package for Probabilistic Modeling and Binning of Metagenomes

Detect complete HGT event rapidly and accurately from complex metagenomics data

Integratedlearner ⭐ 6

Integrated Machine Learning for Multi-omics Classification and Prediction

Mikrokondo ⭐ 6

A simple pipeline for bacterial assembly and quality control

Pangea Plus ⭐ 5

A new implementation of PANGEA pipeline for metagenomics with multiple classification methods and consensus analysis

Curatedmetagenomicsnextflow ⭐ 5

Curated Metagenomics Data Nextflow workflows

MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data; MegaPath-Amplicon: filtering module for metagenomic amplicon data

Main repository of the Flint project for Spark and Amazon EMR.

Microbialgenomemetagenomecourse ⭐ 5

Bioinformatic course on bacterial genomics and metagenomics Helsinki December 2017

Metasequencing ⭐ 5

A metagenomics pipeline using the CGAT framework.

Deepmicrobes ⭐ 5

DeepMicrobes: a deep learning architecture for taxonomic classification of shotgun metagenomic reads

Sars Cov2_analysis ⭐ 5

Documentation for analyzing SARS-Cov2 samples.

Metagenomics Tutorials ⭐ 5

Additional scripts from tutorials on tylerbarnum.com

Knime_seqan_workflows ⭐ 5

KNIME example workflows for NGS data analysis with SeqAn apps.

Pipelines ⭐ 5

Conveyor-based analysis pipelines for metagenome data

Pipeline to pull microbial reads from WGS data and perform metagenomic analysis

Mgnify Web ⭐ 5

Parent repo for MGnify's (EMBL-EBI's metagenomics platform) API and web client. Designed for local development.

Metabolicprofile_inferring ⭐ 5

Metagenomic functional annotation pipeline

Melon: metagenomic long-read-based taxonomic identification and quantification

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

Ancient DNA Read Simulator for Metagenomic

Metagenomics ⭐ 5

Snakemake workflow for functional analysis of metagenomic WGS read data.

🦠🧬 Unraveling Viral Genomes from Metagenomes

Plasmidpicker ⭐ 5

Software to identify plasmid sequence data from metagenome using logistic regression and Minhash

Bioinformatics_pipeline ⭐ 5

Bioinformatics Pipeline

Benchmarkmicrobiome ⭐ 5

Large-scale Benchmarking of Microbial Multivariable Association Methods

Topic Metagenomics ⭐ 5

A repository for the lessons and notebooks used for Binder tutorials

Benchdamic ⭐ 5

Benchmark of differential abundance methods on microbiome data

Nbis Meta ⭐ 5

A snakemake workflow for metagenomic projects

Metagenomics ⭐ 5

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

MetaShot (Metagenomics Shotgun) is a complete pipeline designed for the taxonomic classification of the human microbiota members. In MetaShot, third party tools and new developed Python and Bash scripts are integrated to analyze paired-end (PE) Illumina sequences, offering an automated procedure covering all the analysis steps from raw data management to taxonomic profiling. It is designed to analyze both DNA-Seq and RNA-Seq data.

RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties.

GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and metadata with focus on contamination detection.

Related Searches

Python Metagenomics (148)

Bioinformatics Metagenomics (128)

201-276 of 276 search results

Privacy | About | Terms | Follow Us On Twitter

Copyright 2018-2024 Awesome Open Source. All rights reserved.