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/

MetaGeneMark
FragGeneScan
MetaGeneAnnotator
Orphelia
Metagene

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/

Binning
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)
http://weizhong-lab.ucsd.edu/rammcap/cgi-bin/rammcap.cgi

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/

SOAPZ

MCQ

Online tools for NGS data analysis

parallel Meta see

Sort-Items

PANGEA

Commercial
CLC bio genomic workbench
ERA-7

Quality analysis
FastQC
Prinseq

metagenomics next-gen tutorial • 40k views

ADD COMMENT • link •

modified 6 weeks ago by MetaTK • 10 • written 5.8 years ago by vijay • 1.4k

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

ADD REPLY • link modified 3.1 years ago • written 3.1 years ago by ofanoyi • 110

This an awesome list!

ADD REPLY • link written 5.8 years ago by Istvan Albert ♦♦ 77k

Galaxy is convenient

ADD REPLY • link written 5.2 years ago by psykl2008 • 0

Hi,

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

Thanks

Ali

ADD REPLY • link written 3.7 years ago by invinciblepatriot85 • 20

4.0 years ago by

Tim • 110

United Kingdom

Tim • 110 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 COMMENT • link written 4.0 years ago by Tim • 110

5.2 years ago by

sarahhunter • 600

Cambridge, UK

sarahhunter • 600 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 COMMENT • link written 5.2 years ago by sarahhunter • 600

4.7 years ago by

Csaba Kerepesi • 320

Hungary

Csaba Kerepesi • 320 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 COMMENT • link modified 3.9 years ago • written 4.7 years ago by Csaba Kerepesi • 320

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

ADD REPLY • link written 6 weeks ago by f.a.galkin • 0

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

ADD REPLY • link written 3 days ago by Kevin Blighe ♦ 28k

4.4 years ago by

ofanoyi • 110

Knoxville

ofanoyi • 110 wrote:

MetAMOS

http://genomebiology.com/2013/14/1/R2

https://github.com/marbl/metAMOS

http://metamos.readthedocs.org/en/latest/

ADD COMMENT • link written 4.4 years ago by ofanoyi • 110

3.9 years ago by

geek_y ♦ 8.7k

geek_y ♦ 8.7k wrote:

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

http://chiulab.ucsf.edu/surpi/

http://genome.cshlp.org/content/early/2014/05/16/gr.171934.113.full.pdf+html

ADD COMMENT • link written 3.9 years ago by geek_y ♦ 8.7k

2.8 years ago by

camachofrancine • 80

United States

camachofrancine • 80 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 COMMENT • link modified 2.8 years ago • written 2.8 years ago by camachofrancine • 80

3.5 years ago by

Simply Bioinformatics • 110

WashingtonDC

Simply Bioinformatics • 110 wrote:

Hi,

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 COMMENT • link written 3.5 years ago by Simply Bioinformatics • 110

23 months ago by

glihm • 560

France

glihm • 560 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 COMMENT • link written 23 months ago by glihm • 560

12 months ago by

Simply Bioinformatics • 110

WashingtonDC

Simply Bioinformatics • 110 wrote:

16S Metagenomics:

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

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

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

ADD COMMENT • link modified 10 months ago • written 12 months ago by Simply Bioinformatics • 110

10 months ago by

aim • 10

aim • 10 wrote:

Recent input

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

ViraPipe in github

ADD COMMENT • link written 10 months ago by aim • 10

7 months ago by

haro • 230

France

haro • 230 wrote:

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

ADD COMMENT • link written 7 months ago by haro • 230

7 months ago by

Leonardo Normando • 50

Brazil

Leonardo Normando • 50 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 COMMENT • link modified 7 months ago • written 7 months ago by Leonardo Normando • 50

5 months ago by

hmurray • 20

hmurray • 20 wrote:

You can try gaia.sequentiabiotech.com for free

ADD COMMENT • link written 5 months ago by hmurray • 20

3 months ago by

ricardofull • 0

ricardofull • 0 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 COMMENT • link modified 3 months ago • written 3 months ago by ricardofull • 0

11 weeks ago by

apaytuvi • 20

apaytuvi • 20 wrote:

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

ADD COMMENT • link written 11 weeks ago by apaytuvi • 20

Please mention that your tool is commercial and not FOSS.

ADD REPLY • link written 11 weeks ago by RamRS ♦ 17k

6 weeks ago by

f.a.galkin • 0

Germany

f.a.galkin • 0 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 COMMENT • link written 6 weeks ago by f.a.galkin • 0

6 weeks ago by

MetaTK • 10

MetaTK • 10 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 COMMENT • link written 6 weeks ago by MetaTK • 10

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 REPLY • link written 6 weeks ago by RamRS ♦ 17k

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 REPLY • link written 5 weeks ago by MetaTK • 10

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

ADD REPLY • link written 5 weeks ago by RamRS ♦ 17k

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MetAMOS

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

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.

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