Tutorial: Tools For Metagenomic Data Analysis
88
gravatar for vijay
5.6 years ago by
vijay1.4k
Chennai
vijay1.4k 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/

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

ADD COMMENTlink modified 15 days ago by ricardofull0 • written 5.6 years ago by vijay1.4k
2

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

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by ofanoyi110

This an awesome list!

ADD REPLYlink written 5.6 years ago by Istvan Albert ♦♦ 77k

Galaxy is convenient

ADD REPLYlink written 4.9 years ago by psykl20080
7
gravatar for Tim
3.8 years ago by
Tim110
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 3.8 years ago by Tim110
5
gravatar for sarahhunter
4.9 years ago by
sarahhunter590
Cambridge, UK
sarahhunter590 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 4.9 years ago by sarahhunter590
4
4
gravatar for ofanoyi
4.2 years ago by
ofanoyi110
Knoxville
ofanoyi110 wrote:

MetAMOS

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

https://github.com/marbl/metAMOS

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

ADD COMMENTlink written 4.2 years ago by ofanoyi110
2
gravatar for geek_y
3.6 years ago by
geek_y8.6k
geek_y8.6k 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 COMMENTlink written 3.6 years ago by geek_y8.6k
2
gravatar for camachofrancine
2.6 years ago by
United States
camachofrancine80 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 2.6 years ago • written 2.6 years ago by camachofrancine80
1
gravatar for Simply Bioinformatics
3.3 years ago by
WashingtonDC
Simply Bioinformatics80 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 COMMENTlink written 3.3 years ago by Simply Bioinformatics80
1
gravatar for glihm
20 months ago by
glihm560
France
glihm560 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 20 months ago by glihm560
1
gravatar for Simply Bioinformatics
9 months ago by
WashingtonDC
Simply Bioinformatics80 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 7 months ago • written 9 months ago by Simply Bioinformatics80
1
gravatar for aim
7 months ago by
aim10
aim10 wrote:

Recent input

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

ViraPipe in github

ADD COMMENTlink written 7 months ago by aim10
0
gravatar for invinciblepatriot85
3.4 years ago by
invinciblepatriot8520 wrote:

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 COMMENTlink written 3.4 years ago by invinciblepatriot8520
0
gravatar for Leonardo Normando
4 months ago by
Brazil
Leonardo Normando40 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 4 months ago • written 4 months ago by Leonardo Normando40
0
gravatar for haro
4 months ago by
haro220
France
haro220 wrote:

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

ADD COMMENTlink written 4 months ago by haro220
0
gravatar for hmurray
7 weeks ago by
hmurray20
hmurray20 wrote:

You can try gaia.sequentiabiotech.com for free

ADD COMMENTlink written 7 weeks ago by hmurray20
0
gravatar for ricardofull
15 days ago by
ricardofull0 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 15 days ago • written 15 days ago by ricardofull0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 975 users visited in the last hour