NeSSM / NeSSMt – Next-generation Sequencing Simulator for Metagenomics / Metatranscriptomics

NeSSM / NeSSMt

:: DESCRIPTION

NeSSM is a tool to generate Next-Generation Sequencing (NGS) reads with parameters set by users. The goal of NeSSM is to generate metagenome sequencing reads close to the reality.

NeSSMt is a metatranscriptome simulator. Using a composition table and reference transcripts or genomes (with annotation file)

::DEVELOPER

Dr. Chaochun Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  NeSSM / NeSSMt

:: MORE INFORMATION

Citation:

PLoS One. 2013 Oct 4;8(10):e75448. doi: 10.1371/journal.pone.0075448. eCollection 2013.
NeSSM: a Next-generation Sequencing Simulator for Metagenomics.
Jia B1, Xuan L, Cai K, Hu Z, Ma L, Wei C.

TreeLign / FastTreeLign – Automatic update of 16s rRNA Phylogenetic Tree and Multiple Sequence Alignment in Metagenomics

TreeLign / FastTreeLign

:: DESCRIPTION

TreeLign is automatic update of 16s rRNA phylogenetic tree and multiple sequence alignment in metagenomics

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler
  • Perl

:: DOWNLOAD

 TreeLign

:: MORE INFORMATION

MOCAT2 2.0 – Analyzing Metagenomics Datasets

MOCAT2 2.0

:: DESCRIPTION

MOCAT (Metagenomics Analysis Toolkit) is a package for analyzing metagenomics datasets. Currently MOCAT supports Illumina single- and paired-end reads in raw FastQ format. Using MOCAT you can, for example, generate taxonomic profiles of, and assemble, metagenomes.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 MOCAT

:: MORE INFORMATION

Citation:

MOCAT2: a metagenomic assembly, annotation and profiling framework.
Kultima JR, Coelho LP, Forslund K, Huerta-Cepas J, Li SS, Driessen M, Voigt AY, Zeller G, Sunagawa S, Bork P.
Bioinformatics. 2016 Aug 15;32(16):2520-3. doi: 10.1093/bioinformatics/btw183.

PLoS One. 2012;7(10):e47656. doi: 10.1371/journal.pone.0047656. Epub 2012 Oct 17.
MOCAT: a metagenomics assembly and gene prediction toolkit.
Kultima JR, Sunagawa S, Li J, Chen W, Chen H, Mende DR, Arumugam M, Pan Q, Liu B, Qin J, Wang J, Bork P.

FMAP – Functional Mapping and Analysis Pipeline for Metagenomics and Metatranscriptomics studies

FMAP

:: DESCRIPTION

FMAP (Functional Mapping and Analysis Pipeline) is an open-sourced, stand-alone functional analysis pipeline for analyzing whole metagenomic and metatranscriptomic sequencing data.

::DEVELOPER

The Quantitative Biomedical Research Center 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Perl

:: DOWNLOAD

FMAP

:: MORE INFORMATION

Citation

Kim J, Kim MS, Koh AY, Xie Y, Zhan X.
FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies
BMC Bioinformatics. 2016 Oct 10;17(1):420.PMID: 27724866

MG-RAST 3.5.10 – Metagenomics Analysis Server

MG-RAST 3.5.10

:: DESCRIPTION

MG-RAST (the Metagenomics RAST) server is an automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data.

::DEVELOPER

Folker Meyer, Argonne National Laboratory,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MySQL
  • PostGres
  • Perl
  • R package
  • Apache

:: DOWNLOAD

  MG-RAST

:: MORE INFORMATION

Citation

The Metagenomics RAST server – A public resource for the automatic phylogenetic and functional analysis of metagenomes
F. Meyer, D. Paarmann, M. D’Souza, R. Olson , E. M. Glass, M. Kubal, T. Paczian , A. Rodriguez , R. Stevens, A. Wilke, J. Wilkening, R. A. Edwards
BMC Bioinformatics 2008, 9:386 ,

MetaPath 0.83 – Comparative Analysis of Metabolic Pathways in Metagenomics

MetaPath 0.83

:: DESCRIPTION

MetaPath can identify differentially abundant pathways in metagenomic data-sets, relying on a combination of metagenomic sequence data and prior metabolic pathway knowledge.

::DEVELOPER

Bo Liu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

MetaPath

:: MORE INFORMATION

Citation:

Liu B, Pop M:
Identifying Differentially Abundant Metabolic Pathways in Metagenomic Datasets.
Lect Notes Comput Sci 2010, 6053: 101-112

TANGO 1.0 – Taxonomic Assignment in Metagenomics

TANGO 1.0

:: DESCRIPTION

TANGO  is a tool for the optimal taxonomic assignment of ambiguous pyrosequencing reads.

::DEVELOPER

Jose C. Clemente , Jesper JanssonGabriel Valiente

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Perl

:: DOWNLOAD

 TANGO

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Jan 1;30(1):17-23. doi: 10.1093/bioinformatics/btt256. Epub 2013 May 3.
Further steps in TANGO: improved taxonomic assignment in metagenomics.
Alonso-Alemany D1, Barré A, Beretta S, Bonizzoni P, Nikolski M, Valiente G.

BMC Bioinformatics. 2011 Jan 7;12:8. doi: 10.1186/1471-2105-12-8.
Flexible taxonomic assignment of ambiguous sequencing reads.
Clemente JC, Jansson J, Valiente G.

MTR – Metagenomics software for Clustering at multiple ranks

MTR

:: DESCRIPTION

MTR is a new method for tackling the drawbacks using clustering at Multiple Taxonomic Ranks.

::DEVELOPER

Fabio Gori

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • C++ Complier
  • MatLab

:: DOWNLOAD

 MTR

:: MORE INFORMATION

Citation

Fabio Gori, Gianluigi Folino, Mike S. M. Jetten, and Elena Marchiori.
MTR: Taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks.
Bioinformatics (2011) 27 (2): 196-203.doi: 10.1093/bioinformatics/btq649

Omega 1.0.2 – Overlap-graph de novo Assembler for Metagenomics

Omega 1.0.2

:: DESCRIPTION

Omega is a software for assembling and scaffolding Illumina sequencing data of microbial communities.

::DEVELOPER

Omics Bio

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Omega

:: MORE INFORMATION

Citation

Omega: an Overlap-graph de novo Assembler for Metagenomics.
Haider B, Ahn TH, Bushnell B, Chai J, Copeland A, Pan C.
Bioinformatics. 2014 Jun 19. pii: btu395.

Metarep 1.4.0 – High-performance Comparative Metagenomics Tool

Metarep 1.4.0

:: DESCRIPTION

METAREP (JCVI Metagenomics Reports) is a new open source tool for high-performance comparative metagenomics. It provides a suite of web based tools to help scientists to view, query, browse and compare metagenomics annotation data derived from ORFs called on metagenomics reads.

METAREP supports browsing of functional and taxonomic assignments. Users can either specify fields, or logical combinations of fields to flexibly filter datasets on the fly. Users can compare multiple datasets at various functional and taxonomic levels applying statistical tests as well as hierarchical clustering, multidimensional scaling and heatmaps.

::DEVELOPER

J. Craig Venter Institute

:: SCREENSHOTS

 

:: REQUIREMENTS

:: DOWNLOAD

Metarep

:: MORE INFORMATION

Citation:

Johannes Goll etc.
METAREP: JCVI metagenomics reports—an open source tool for high-performance comparative metagenomics
Bioinformatics (2010) 26 (20): 2631-2632.