Tutorial:Tools For Metagenomic Data Analysis

Question

[vijay]

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
• Celera
• Metasim (Simulator-used to compare predictions)
• Euler
• JAZZ

Gene calling

• genemark.hmm (using HMM models to identify genes)
• MetaGeneMark
• FragGeneScan
• MetaGeneAnnotator
• Orphelia
• Metagene

Microbial diversity Analysis

• MLST
• MOTHUR
• EstimateS
• QIIME
• PHACCS

Binning

Composition based binning

• TETRA
• Phylopathia

Sequence similiarity based binning

• MEGAN
• CARMA
• Phymm

Functional Annotation

• MEX (Motif Extraction)
• MG-RAST
• RAMMCAP (Rapid analysis of Multiple Metagenomes with Clustering and Annotation Pipeline)

Comparative Metagenomics

• MEGAN
• MG-RAST
• Camera
• ShotgunFunctionalizeR
• UniFrac
• MetaStats
• Galaxy
• MetaMine
• MetaLook
• IMG/M

Mapping to reference genome

• Bowtie
• BWA
• 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

[ofanoyi]

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

[Istvan Albert]

This an awesome list!

[psykl2008]

Galaxy is convenient

[invinciblepatriot85]

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

[Shicheng Guo]

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

[Shicheng Guo]

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

[Shicheng Guo]

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

Answer 1

[Tim]

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.

Answer 2

[sarahhunter]

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.

Answer 3

[Csaba Kerepesi]

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

[f.a.galkin]

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

[Kevin Blighe]

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

[Bramadi Arya]

Looks like this is a different FANTOM. The first FANTOM is a functional and taxonomic analysis of metagenomes. In contrast, the other one is FANTOM (Functional ANnoTation Of the Mammalian genome) in the fields of transcriptome analysis. Please correct me if I was mistaken.

Answer 4

[ofanoyi]

MetAMOS

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

https://github.com/marbl/metAMOS

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

Answer 5

[GouthamAtla]

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

Answer 6

[frcamacho]

Cool new profiler tool for metagenomic data, 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.

Answer 7

[Simply Bioinformatics]

16S Metagenomics:

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

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

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

Answer 8

[Simply Bioinformatics]

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/

Answer 9

[glihm]

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.

Answer 10

[aim]

Recent input

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

ViraPipe in github

Answer 11

[Leonardo Normando]

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."

Answer 12

[vmicrobio]

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

Answer 13

[hmurray]

You can try gaia.sequentiabiotech.com for free

Answer 14

[ricardofull]

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.

Answer 15

[apaytuvi]

Gaia for analyzing both amplicon and shotgun metagenomics (including metatranscriptomics). Everything's done online.

[Ram]

Please mention that your tool is commercial and not FOSS.

[alfonsosaera]

Great tool! I really recommend it.

Answer 16

[f.a.galkin]

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.

Answer 17

[MetaTK]

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.

[Ram]

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.

[MetaTK]

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.

[Ram]

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

[krushnach80]

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

[DMA]

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.

Answer 18

[juanjo75es]

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

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