Tutorial: Tools For Metagenomic Data Analysis
gravatar for vijay
8.2 years ago by
vijay1.6k wrote:

Dear All,

I just thought it would be worthwhile posting this , as it would be beneficial for those who are stepping into field of metagenomics . Below are the compiled list of tools and links to a few of them , that can be used for primary and secondary analysis of metagenomic sequence data.(Though there are plenty missed out here..)

Please do add to this list, as the list will be ever growing...:)

Metagenome assembly
Velvet http://www.ebi.ac.uk/~zerbino/velvet/ Celera http://www.cbcb.umd.edu/research/assembly.shtml#software Metasim(Simulator-used to compare predictions) http://ab.inf.uni-tuebingen.de/software/metasim/welcome.html#Download Euler http://nbcr.sdsc.edu/euler/ JAZZ

Gene calling
genemark.hmm(using HMM models to identify genes) http://exon.gatech.edu/GeneMark/metagenome/Prediction/


Microbial diversity Analysis

MLST(http://www. mlst.net) http://www.mlst.net/

MOTHUR http://www.mothur.org/

EstimateS http://viceroy.eeb.uconn.edu/EstimateS/

QIIME http://qiime.org/install/virtual_box.html

PHACCS http://phaccs.sourceforge.net/

Composition based binning
TETRA http://www.megx.net/tetra/index.html

Phylopathia http://cbcsrv.watson.ibm.com/phylopythia.html

Sequence similiarity based binning
MEGAN http://ab.inf.uni-tuebingen.de/software/megan/

CARMA http://www.cebitec.uni-bielefeld.de/brf/carma/carma.html

Phymm http://www.cbcb.umd.edu/software/phymm/

Functional Annotation
MEX(Motif Extraction) http://adios.tau.ac.il/SPMatch/

MG-RAST http://metagenomics.anl.gov/

RAMMCAP(Rapid analysis of Multiple Metagenomes with Clustering and Annotation Pipeline)

Comparitive Metagenomics
MEGAN http://metagenomics.anl.gov/

MG-RAST http://metagenomics.anl.gov/

Camera http://camera.calit2.net/#

ShotgunFunctionalizeR http://shotgun.math.chalmers.se/

UniFrac http://bmf.colorado.edu/unifrac/

MetaStats http://metastats.cbcb.umd.edu/detection.html

Galaxy https://main.g2.bx.psu.edu/u/aun1/w/metagenomic-analysis

MetaMine http://www.megx.net/metamine/

MetaLook http://www.megx.net/metalook/index.php

IMG/M http://img.jgi.doe.gov/cgi-bin/m/main.cgi

Mapping to reference genome

Bowtie http://bowtie-bio.sourceforge.net/index.shtml

BWA http://bio-bwa.sourceforge.net/



Online tools for NGS data analysis

parallel Meta see



CLC bio genomic workbench

Quality analysis

ADD COMMENTlink modified 2.5 years ago by MetaTK20 • written 8.2 years ago by vijay1.6k

It seems that many links did not work anymore. Maybe some updates will help. Thanks.

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by ofanoyi120

This an awesome list!

ADD REPLYlink written 8.2 years ago by Istvan Albert ♦♦ 86k

Galaxy is convenient

ADD REPLYlink written 7.6 years ago by psykl20080


I am working on Metagenomics data. I am trying to predict promoters after assembly. I would appreciate if someone can suggest any good tool.


ADD REPLYlink modified 12 months ago by _r_am32k • written 6.0 years ago by invinciblepatriot8520

Can you share some mature analysis pipeline to solve the most common metagenomic questions?

ADD REPLYlink written 12 months ago by Shicheng Guo8.5k

Thanks Vijay, you shared several different metagenome assembly? which one is the most welcomed?

ADD REPLYlink written 12 months ago by Shicheng Guo8.5k

Hi Vijay, Some collection to toxic genes/transcript from all the metagenomics references?

ADD REPLYlink written 12 months ago by Shicheng Guo8.5k
gravatar for Tim
6.4 years ago by
United Kingdom
Tim110 wrote:

Just to add my two pennies worth - pipelines for analysis of viromes:

VIROME: classification of predicted open-reading frames (ORFs) from viral metagenomes

METAVIR/METAVIR 2: tools for viral metagenome comparison and assembled virome analysis

Take a look at VMGAP and ProViDE as well.

ADD COMMENTlink written 6.4 years ago by Tim110
gravatar for sarahhunter
7.6 years ago by
Cambridge, UK
sarahhunter600 wrote:

May I add a plug for http://www.ebi.ac.uk/metagenomics? We have developed a pipeline for taxonomic and functional analysis of metagenomic samples and we also archive your raw sequence data in the SRA on your behalf. We're always looking for suggestions of how to improve our service, so please contact us with feedback. We will be launching new features on our website later next month and hope to publish the resource in NAR database issue this year.

ADD COMMENTlink written 7.6 years ago by sarahhunter600
gravatar for Csaba Kerepesi
7.0 years ago by
Csaba Kerepesi330 wrote:

Other (new) tools for metagenomic analysis:

AmphoraNet: metagenomic analysis webserver

AmphoraVizu: Chart visualization webserver for metagenomics analysis tools AMPHORA2 and AmphoraNet

FANTOM: functional and taxonomic analysis of metagenomes

MetaPhlAn: metagenomic phylogenetic analysis

ADD COMMENTlink modified 6.3 years ago • written 7.0 years ago by Csaba Kerepesi330

Is FANTOM alive? Their download and manual links aren't working for me

ADD REPLYlink written 2.5 years ago by f.a.galkin40

Yes, very much alive: http://fantom.gsc.riken.jp/

ADD REPLYlink written 2.4 years ago by Kevin Blighe69k
gravatar for ofanoyi
6.8 years ago by
ofanoyi120 wrote:





ADD COMMENTlink written 6.8 years ago by ofanoyi120
gravatar for geek_y
6.2 years ago by
geek_y11k wrote:

SURPI: Pipeline for pathogen identification from complex metagenomic NGS data.





ADD COMMENTlink written 6.2 years ago by geek_y11k
gravatar for frcamacho
5.2 years ago by
United States
frcamacho190 wrote:

Cool new profiler tool for metagenomic data, ShortBRED (https://huttenhower.sph.harvard.edu/shortbred).

ShortBRED is a pipeline to take a set of protein sequences, group them into families, extract a set of distinctive strings ("markers"), and then search for these markers in metagenomic data and determine the presence and abundance of the protein families of interest.


ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by frcamacho190
gravatar for Simply Bioinformatics
3.4 years ago by
Simply Bioinformatics180 wrote:

16S Metagenomics:

Mothur: https://www.mothur.org/wiki/Category:Commands

Usearch: http://www.drive5.com/usearch/manual/

Qiime: http://qiime.org/scripts/

ADD COMMENTlink modified 3.2 years ago • written 3.4 years ago by Simply Bioinformatics180
gravatar for Simply Bioinformatics
5.9 years ago by
Simply Bioinformatics180 wrote:


I recently find these two software pretty useful :

Gene Calling:

prodigal  : http://prodigal.ornl.gov/server.html

pathway and function prediction:

picrust : http://picrust.github.io/picrust/


ADD COMMENTlink written 5.9 years ago by Simply Bioinformatics180
gravatar for glihm
4.3 years ago by
glihm620 wrote:

In the category "Microbial Diversity Analysis":

A very nice and frequently updated program in order to pick OTU from 16S rRNA gene amplicons sequencing: USEARCH (http://www.drive5.com/usearch/).

It is not user-friendly (command line), but the documentation is nice and the tools well adapter and flexible.

ADD COMMENTlink written 4.3 years ago by glihm620
gravatar for aim
3.2 years ago by
aim10 wrote:

Recent input

ViraPipe: Scalable Parallel Pipeline for Viral Metagenome Analysis from Next Generation Sequencing Reads

ViraPipe in github

ADD COMMENTlink written 3.2 years ago by aim10
gravatar for Leonardo Normando
3.0 years ago by
Leonardo Normando60 wrote:

Check this out: https://omictools.com/metagenomics-category They manage a curated list of bioinformatics tools.

From their site: "OMICtools strives to accelerate research in bioinformatics, making tools accessible to everyone and offering a stimulating work environment to assist life scientists extracting new findings from the omics data."

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Leonardo Normando60
gravatar for vmicrobio
3.0 years ago by
vmicrobio270 wrote:

Have a look on Mash Screen, I found it usefull and easy to use!

ADD COMMENTlink written 3.0 years ago by vmicrobio270
gravatar for hmurray
2.8 years ago by
hmurray30 wrote:

You can try gaia.sequentiabiotech.com for free

ADD COMMENTlink written 2.8 years ago by hmurray30
gravatar for ricardofull
2.7 years ago by
ricardofull10 wrote:

16S Metagenomics:

in R

-DADA2 to Filter, quality analysis, trimming, Merge Runs, Remove Chimeras, Assign Taxonomy Phyloseq to

-Phyloseq to a deeper analysis of metagenomic data.

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by ricardofull10
gravatar for apaytuvi
2.6 years ago by
apaytuvi40 wrote:

Gaia (https://metagenomics.sequentiabiotech.com/) for analyzing both amplicon and shotgun metagenomics (including metatranscriptomics). Everything's done online.

ADD COMMENTlink written 2.6 years ago by apaytuvi40

Please mention that your tool is commercial and not FOSS.

ADD REPLYlink written 2.6 years ago by _r_am32k

Great tool! I really recommend it.

ADD REPLYlink written 22 months ago by alfonsosaera20
gravatar for f.a.galkin
2.5 years ago by
f.a.galkin40 wrote:

I really liked using Centrifuge for WGS taxonomic profiling.
It is resource efficient (has a 6GB index for all bacteria, compared to Kraken's over 100GB) and produces an abundance table when it's finished.

ADD COMMENTlink written 2.5 years ago by f.a.galkin40
gravatar for MetaTK
2.5 years ago by
MetaTK20 wrote:

16S rRNA metagenomics:

I tried DocMind Analyst on the AWS cloud and found it very convenient and easy to use. It works with a graphical user interface and uses mothur and RDP for read processing and classification. Their tutorials are also very good for beginners.

ADD COMMENTlink written 2.5 years ago by MetaTK20

You seem to be advertising docmind analytics. I'd recommend you create a Tool type post and explain this tool, including its pricing strategy. The website is confusing on what is free and what their pricing system is. Please do not bulk-add answers recommending this tool.

ADD REPLYlink written 2.5 years ago by _r_am32k

Thanks for your comment, Ram. I am not affiliated with the company but I know the owner. So I guess I have a conflict of interest. However, I really like his idea and software, particularly for non-expert in computer science (I consider myself as such). That's why I am positive about it. I have forwarded your recommendation regarding a tool type post and publishing a clear pricing policy.

ADD REPLYlink written 2.4 years ago by MetaTK20

Thank you for doing that, it's the right way to go about it! I look forward to learning more about this tool.

ADD REPLYlink written 2.4 years ago by _r_am32k

lots of resources to look for ..so a simple question this should work both whole genome as well as 16s RNA meta-genomic analysis ?

ADD REPLYlink written 2.3 years ago by krushnach80870

At the moment it works only for 16S rRNA sequencing. But soon shotgun metagenomics analysis will be implemented. I will submit a little overview over all its functions soon in the tool section.

ADD REPLYlink written 2.2 years ago by DMA20
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