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Tools For Metagenomic Data Analysis  

2014-12-17 06:37:28|  分类: 默认分类 |  标签: |举报 |字号 订阅

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cited from https://www.biostars.org/p/58279/ 
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


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

https://github.com/marbl/metAMOS

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