Quality analysis
FastQC
Prinseq
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.unituebingen.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
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
Online tools for NGS data analysis
CONTIGuator: bacterial genomes finishing tool http://contiguator.sourceforge.net/
parallel Meta see
Sort-Items
PANGEA
http://www.ebi.ac.uk/metagenomics
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
Commercial
CLC bio genomic workbench
ERA-7