Tutorial:Tools For Metagenomic Data Analysis
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8.4 years ago
vijay ★ 1.6k

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/

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 Tutorial • 50k views
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2
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It seems that many links did not work anymore. Maybe some updates will help. Thanks.

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0
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This an awesome list!

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0
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Galaxy is convenient

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0
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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

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0
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Can you share some mature analysis pipeline to solve the most common metagenomic questions?

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0
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Thanks Vijay, you shared several different metagenome assembly? which one is the most welcomed?

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0
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Hi Vijay, Some collection to toxic genes/transcript from all the metagenomics references?

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7
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6.6 years ago
Tim ▴ 110

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.

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5
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7.8 years ago
sarahhunter ▴ 600

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.

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4
0
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Is FANTOM alive? Their download and manual links aren't working for me

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0
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Yes, very much alive: http://fantom.gsc.riken.jp/

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2
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6.5 years ago

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

 

 

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2
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5.4 years ago
frcamacho ▴ 190

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.

 

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6.1 years ago

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/

 

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1
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4.5 years ago
glihm ▴ 620

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.

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3.2 years ago

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."

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1
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3.2 years ago
vmicrobio ▴ 270

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

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3.0 years ago
hmurray ▴ 30

You can try gaia.sequentiabiotech.com for free

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2.9 years ago
ricardofull ▴ 10

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.

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2.8 years ago
apaytuvi ▴ 40

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

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1
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Please mention that your tool is commercial and not FOSS.

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0
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Great tool! I really recommend it.

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2.7 years ago
f.a.galkin ▴ 40

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.

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2.7 years ago
MetaTK ▴ 20

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.

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0
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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.

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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.

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

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0
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lots of resources to look for ..so a simple question this should work both whole genome as well as 16s RNA meta-genomic analysis ?

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0
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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.

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4 weeks ago
juanjo75es ▴ 120

For virome assembly, the best results are obtained with s-aligner. It gets at least 64% larger NG50 than the second best.

enter image description here

Source: "s-aligner: a greedy algorithm for non-greedy denovo genome assembly"

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