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Workflow software tools | Shotgun metagenomic sequencing data analysis

These pipeline and workflow tools provide out-of-the box solutions for metagenomic analysis by chaining a number of specific analysis tools together.

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QIIME
Desktop

QIIME Quantitative Insights Into Microbial Ecology

An open source software package for comparison and analysis of microbial…

An open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data, but also supporting analysis of other types of data.

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AMPHORA
Web
Desktop

AMPHORA AutoMated PHylogenomic infeRence Application

Allows genome tree reconstruction and metagenomic phylotyping. AMPHORA is an…

Allows genome tree reconstruction and metagenomic phylotyping. AMPHORA is an application for large-scale protein phylogenetic analysis. The software supports the analyses of DNA sequences, which…

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MOCAT
Desktop

MOCAT

A software pipeline for metagenomic sequence assembly and gene prediction with…

A software pipeline for metagenomic sequence assembly and gene prediction with novel features for taxonomic and functional abundance profiling. The automated generation and efficient annotation of…

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AmrPlusPlus
Desktop

AmrPlusPlus

A user-friendly Galaxy pipeline for the analysis of high throughput sequencing…

A user-friendly Galaxy pipeline for the analysis of high throughput sequencing data that is pre-packaged for use with the MEGARes database. AmrPlusPlus not only increases the accessibility of…

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phyloseq
Desktop

phyloseq

A package dedicated to the object-oriented representation and analysis of…

A package dedicated to the object-oriented representation and analysis of microbiome census data in R. Phyloseq supports importing data from a variety of common formats, as well as many analysis…

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IMP
Desktop

IMP Integrated Meta-omic Pipeline

Is developed to perform large-scale, reproducible and automated integrative…

Is developed to perform large-scale, reproducible and automated integrative reference free analysis of metagenomic and metatranscriptomic data. IMP incorporates robust read preprocessing, iterative…

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Parallel-META
Desktop

Parallel-META

Provides rapid data mining on taxonomy and metabolic function across a large…

Provides rapid data mining on taxonomy and metabolic function across a large number of metagenome datasets. Parallel-META is useful for: (1) vector-graph-based visualization and parallel computing;…

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mothur
Desktop

mothur

Aims to be a comprehensive software package that allows users to use a single…

Aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. mothur builds upon previous tools to provide a flexible and…

iVirus
Dataset

iVirus

Leverages the CyVerse cyberinfrastructure to provide access to viromic tools…

Leverages the CyVerse cyberinfrastructure to provide access to viromic tools and data sets. The iVirus Data Commons contains both raw and processed data from 1866 samples and 73 projects derived from…

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Rhea
Desktop

Rhea

Encodes a series of well documented choices for the downstream analysis of…

Encodes a series of well documented choices for the downstream analysis of Operational Taxonomic Units (OTUs) tables, including normalization steps, alpha- and beta-diversity analysis, taxonomic…

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ShortBRED
Desktop

ShortBRED Short Better Representative Extract Dataset

Facilitates fast, accurate functional profiling of metagenomic samples.…

Facilitates fast, accurate functional profiling of metagenomic samples. ShortBRED consists of two components: (i) a method that reduces reference proteins of interest to short, highly representative…

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drVM
Desktop

drVM detect and reconstruct known viral genomes from metagenomes

Allows rapid viral read identification, genus-level read partition, read…

Allows rapid viral read identification, genus-level read partition, read normalization, de novo assembly, sequence annotation and coverage profiling. In drVM, the first two procedures and sequence…

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WebMGA
Desktop
Web

WebMGA

A customizable web server for fast metagenomic analysis. WebMGA includes over…

A customizable web server for fast metagenomic analysis. WebMGA includes over 20 commonly used tools such as ORF calling, sequence clustering, quality control of raw reads, removal of sequencing…

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Microbiome…
Desktop

Microbiome Helper

Contains several resources to help researchers working with microbial…

Contains several resources to help researchers working with microbial sequencing data. Microbiome Helper is an assortment of scripts to help process and automate various microbiome and metagenomic…

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metakallisto
Desktop

metakallisto

Allows metagenomic sequence data to be analyzed with the fast, accurate RNA-Seq…

Allows metagenomic sequence data to be analyzed with the fast, accurate RNA-Seq abundance estimator kallisto. Metakallisto contains python scripts and offers functions that compare the output of a…

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FMAP
Desktop

FMAP Functional Mapping and Analysis Pipeline

A stand-alone functional analysis pipeline for analyzing whole metagenomic and…

A stand-alone functional analysis pipeline for analyzing whole metagenomic and metatranscriptomic sequencing data. FMAP performs alignment, gene family abundance calculations, and statistical…

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DECARD
Desktop

DECARD Detailed Evaluation Creation and Analysis of Read Data

Simulates amplicon-based microbiome experiments and tests classification…

Simulates amplicon-based microbiome experiments and tests classification software. DECARD allows to generate realistic synthetic datasets for which there is a known source of the sequences to be used…

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ICoVeR
Desktop

ICoVeR Interactive Contig-bin Verification and Refinement

Allows to visualize genome bins. ICoVeR allows to curate bin assignments based…

Allows to visualize genome bins. ICoVeR allows to curate bin assignments based on multiple binning algorithms. It was tested on the refinement disparate of genome bins automatically generated by…

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SURPI
Desktop

SURPI Sequence-based Ultra-Rapid Pathogen Identification

A computational pipeline for pathogen identification from complex metagenomic…

A computational pipeline for pathogen identification from complex metagenomic next-generation sequencing (NGS) data generated from clinical samples.

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FGP
Web
Desktop

FGP FunGene Pipeline

Houses tools for researchers to process and analyze their own functional gene…

Houses tools for researchers to process and analyze their own functional gene sequencing data. FGP offers a pipeline where researchers can assemble a set of analysis tools to process a nucleotide…

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BMPOS
Desktop

BMPOS Brazilian Microbiome Project Operating System

Allows analysis for metagenomic studies (phylogenetic marker genes). BMPOS is…

Allows analysis for metagenomic studies (phylogenetic marker genes). BMPOS is effective for sequences processing, sequences clustering, alignment, taxonomic annotation, statistical analysis, and…

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MetaStorm
Web

MetaStorm

Offers both read matching and assembly-based annotation pipelines. MetaStorm is…

Offers both read matching and assembly-based annotation pipelines. MetaStorm is an online metagenomic analysis server. It enables customization of reference databases and allows users to upload…

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MetLab
Desktop

MetLab

Provides experimental design and analysis of viral metagenomes. MetLab permits…

Provides experimental design and analysis of viral metagenomes. MetLab permits to design the experiment and provides calculations for the coverage needed. It enables researchers to carefully prepare…

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ViraPipe
Desktop

ViraPipe

Scans viral metagenomes from hundreds of next generation sequencing (NGS)…

Scans viral metagenomes from hundreds of next generation sequencing (NGS) samples. ViraPipe employs data parallel computation strategy. It is able to processes genomic data in partitions at many…

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ASaiM
Desktop

ASaiM Auvergne Sequence analysis of intestinal Microbiota

Provides tools and workflows dedicated to microbiota analyses with an extensive…

Provides tools and workflows dedicated to microbiota analyses with an extensive documentation. ASaiM is an Open-Source opinionated Galaxy-based framework based on four pillars: 1) easy and stable…

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CITESspeciesDet…
Web
Desktop

CITESspeciesDetect

Identifies CITES (the Convention on International Trade in Endangered Species…

Identifies CITES (the Convention on International Trade in Endangered Species of Wild Fauna and Flora) -listed species using Illumina paired-end sequencing technology. CITESspeciesDetect is a…

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Themetagenomics
Desktop

Themetagenomics

Provides a topic model framework for microbiome abundance data, as well as…

Provides a topic model framework for microbiome abundance data, as well as prediction for 16S rRNA survey data. Themetagenomics is a package that offers an R implementation of PICRUSt and wraps…

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MetaMeta
Desktop

MetaMeta

Classifies metagenomic datasets. MetaMeta allows user to obtain more precise or…

Classifies metagenomic datasets. MetaMeta allows user to obtain more precise or sensitive results by providing a single default parameter. It executes and integrates results from metagenome analysis…

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BusyBee Web
Web

BusyBee Web

Serves for the automated, reference-independent binning and visualization of…

Serves for the automated, reference-independent binning and visualization of metagenomic data in the form of assembled contigs or long reads. BusyBee website works about population-level resolved…

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RTK
Desktop

RTK

Performs rarefaction analysis of large count matrices, as well as estimation…

Performs rarefaction analysis of large count matrices, as well as estimation and visualization of diversity, richness and evenness. RTK computes estimates of ecological diversity and provides…

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MetaABC
Desktop

MetaABC Metagenomics platform for data Adjustment Binning and Clustering

Integrates different steps for better estimation of the taxonomic assignment.…

Integrates different steps for better estimation of the taxonomic assignment. MetaABC is an integrated metagenomics platform for data adjustment, binning and clustering. This method incorporates (i)…

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Fungal ITS…
Desktop

Fungal ITS Pipeline

Accelerates the processing of large numbers of query sequences. Fungal internal…

Accelerates the processing of large numbers of query sequences. Fungal internal transcribed spacer (ITS) Pipeline is a package developed to obtain extended functionality helpful for complementary,…

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MePIC
Web

MePIC Metagenomic Pathogen Identification for Clinical specimens

Detects pathogen sequences from metagenome data derived from specimen material…

Detects pathogen sequences from metagenome data derived from specimen material from patients. MePIC will trim low quality data, remove sequence data from hosts (i.e. host patients) and then perform…

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PANGEA
Desktop

PANGEA Pipeline Analysis for Next GEneration Amplicons

A series of bioinformatics tools for high-throughput sequencing analysis,…

A series of bioinformatics tools for high-throughput sequencing analysis, including pre-processing, clustering, database matching, and classification. With PANGEA, sequences obtained directly from…

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vegan
Desktop

vegan

Ordination methods, diversity analysis and other functions for community and…

Ordination methods, diversity analysis and other functions for community and vegetation ecologists.

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Anvi'o
Desktop

Anvi'o analysis and visualization platform for 'omics data

Brings together many aspects of today’s cutting-edge genomic, metagenomic,…

Brings together many aspects of today’s cutting-edge genomic, metagenomic, and metatranscriptomic analysis practices to address a wide array of needs. Anvi’o is an advanced analysis and…

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MetaGeniE
Desktop

MetaGeniE

Generates an all-against-all comparison dataset between the reads and the…

Generates an all-against-all comparison dataset between the reads and the reference database and then uses these results to generate cumulative statistics from combined local and global alignment.…

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IM-TORNADO
Desktop

IM-TORNADO Illinois Mayo Taxon Organization from RNA Dataset Operations

A workflow for processing non-overlapping reads while retaining maximal…

A workflow for processing non-overlapping reads while retaining maximal information content. IM-TORNADO is used for carrying out common microbiome analyses leveraging the information of the paired…

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Nephele
Desktop

Nephele

Aims to address a major challenge facing researchers today — namely,…

Aims to address a major challenge facing researchers today — namely, analyzing, transferring, and storing biomedical "big data" — through the use of cloud-based resources. Nephele is a…

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SOAPBarcode
Desktop

SOAPBarcode

Assembles short Illumina reads into full-length COI barcode sequences.…

Assembles short Illumina reads into full-length COI barcode sequences. SOAPBarcode is a sequencing pipeline that transforms raw Illumina reads into full-length COI barcode sequences. It was coupled…

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META-pipe
Desktop

META-pipe

Allows for marine metagenomics analysis. META-pipe offers preprocessing,…

Allows for marine metagenomics analysis. META-pipe offers preprocessing, assembly, taxonomic classification and functional analysis. To reduce the effort to develop and deploy it, it has been…

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RDPipeline
Desktop
Web

RDPipeline

Aims to simplify the processing of large rRNA sequence libraries (including…

Aims to simplify the processing of large rRNA sequence libraries (including single-strand and paired-end reads) obtained through high-throughput sequencing technology.

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RTG…
Desktop

RTG Metagenomics

Delivers comprehensive results on the composition of microbial communities and…

Delivers comprehensive results on the composition of microbial communities and their associated metabolic pathways, genes and genomes. Real Time Genomics’ metagenomic pipeline was developed to…

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ITScan
Web

ITScan

Automates the analysis of fungal internal transcribed spacer (ITS) sequences…

Automates the analysis of fungal internal transcribed spacer (ITS) sequences generated either by Sanger or Next Generation Sequencing (NGS) platforms. ITScan is an architectural model that can be…

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