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
It seems that many links did not work anymore. Maybe some updates will help. Thanks.
This an awesome list!
Galaxy is convenient
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
Can you share some mature analysis pipeline to solve the most common metagenomic questions?
Thanks Vijay, you shared several different metagenome assembly? which one is the most welcomed?
Hi Vijay, Some collection to toxic genes/transcript from all the metagenomics references?