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Tools For Metagenomic Data Analysis  

2015-03-23 16:59:55|  分类: 生物信息分析 |  标签: |举报 |字号 订阅

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The new field of metagenomics studies the microorganism communities by culture-independent sequencing. With the advances in the next-generation sequencing techniques, scientists are facing tremendous challenges in metagenomic data analysis due to the huge quantity and high complexity of sequence data. Analyzing large datasets is extremely time-consuming. In addition, metagenomic annotation involves a wide range of computational tools. It is very difficult for common users to install and maintain these software packages. The tools provided by the few available web servers are also limited and have various constraints such as login requirement, long waiting time, inability to configure pipelines etc. Here we developed WebMGA, a customizable web server for fast metagenomic analysis. WebMGA includes over 20 commonly used tools for analyses such as ORF calling, sequence clustering, quality control of raw reads, removal of sequencing artifacts and contaminations, taxonomic analysis, functional annotation etc, as shown in the following diagram:

Tools For Metagenomic Data Analysis - 喜欢吃桃子 - wangyufeng的博客

 

Metagenome assembly 
Velvet http://www.ebi.ac.uk/~zerbino/velvet/ Celera http://www.cbcb.umd.edu/research/assembly.shtml#softwareMetasim(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

via:https://www.biostars.org/p/58279/ and http://weizhonglab.ucsd.edu/metagenomic-analysis

 

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