CoMeta 0.3 – Classification of Metagenomes using k-mers

CoMeta 0.3

:: DESCRIPTION

CoMeta is a tool used to assigns a query read (DNA fragment) from metagenomic sample into one of the groups (the most common the taxon).

::DEVELOPER

REFRESH Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 CoMeta

:: MORE INFORMATION

Citation

PLoS One. 2015 Apr 17;10(4):e0121453. doi: 10.1371/journal.pone.0121453. eCollection 2015.
CoMeta: classification of metagenomes using k-mers.
Kawulok J, Deorowicz S

Admixem v1.0.1 – Quality Assessment Tool for Metagenome Assemblies

Admixem v1.0.1

:: DESCRIPTION

Admix’em (Admixture simulator) is a new forward-time simulator that allows for rapid and realistic simulations of admixed populations with selection.

::DEVELOPER

Ray Cui

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX
  • C++ COmpiler

:: DOWNLOAD

 Admixem

:: MORE INFORMATION

Citation

Admix’em: A flexible framework for forward-time simulations of hybrid populations with selection and mate choice.
Cui R, Schumer M, Rosenthal GG.
Bioinformatics. 2015 Nov 28. pii: btv700.

Taxy / Taxy-Pro – Fast Estimation of Metagenomic Taxon Abundances

Taxy / Taxy-Pro

:: DESCRIPTION

Taxy is a software for taxonomic profiling based on mixture modeling of the overall oligonucleotide distribution of a sample. Inferring the taxonomic composition of a microbial community from a large collection of anonymous DNA sequencing reads is a challenging task in computational biology. Because existing methods for taxonomic profiling of metagenomes are all based on the assignment of fragmental sequences to phylogenetic categories, the accuracy of results largely depends on fragment length. This dependency complicates comparative analysis of data originating from different sequencing platforms or preprocessing pipelines. We have developed a read length-independent method for taxonomic profiling and we provide a freely available Matlab/Octave toolbox which includes an ultra-fast implementation of that method. Besides the platform-independent toolbox we also provide a prototype tool implementation for Windows that allows the user to compare a large number of preprocessed metagenomes within a graphical environment.Our tests indicate that Taxy results compare well with taxonomic profiles obtained with other methods. However, in contrast to the existing methods, Taxy provides a nearly constant profiling accuracy across all kinds of read lengths and it operates at an unrivaled speed. As input, DNA sequences in terms of multi-FASTA files of any size can be used for the estimation of metagenomic profiles. The analysis of a large sequence file with a Gbp volume typically requires less than a minute of processing time and can even be performed on a standard notebook.

In contrast to the oligonucleotide-based Taxy method, Taxy-Pro is based on mixture model analysis of protein signatures in terms of protein domain frequencies.

::DEVELOPER

the Department of Bioinformatics of the University of Göttingen

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac OS X / Windows
  • Matlab

:: DOWNLOAD

 Taxy / Taxy-Pro

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Apr 15;29(8):973-80. doi: 10.1093/bioinformatics/btt077. Epub 2013 Feb 15.
Protein signature-based estimation of metagenomic abundances including all domains of life and viruses.
Klingenberg H1, Aßhauer KP, Lingner T, Meinicke P.

P. Meinicke, K. Asshauer and T. Lingner.
Mixture models for analysis of the taxonomic composition of metagenomes“,
Bioinformatics May 15, 2011 27 (10)

GWproxy – Clustering Metagenome Short Reads using Weighted Proteins

GWproxy

:: DESCRIPTION

GWproxy is a software for clustering metagenome short reads. The software incorporates biological knowledge in the clustering process, by means of a list of proteins associated to
each read. These proteins are chosen from a reference proteome database according to their similarity with the given read, as evaluated by BLAST.

::DEVELOPER

Fabio Gori

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GWproxy

:: MORE INFORMATION

Citation

Gianluigi Folino, Fabio Gori, Mike S. M. Jetten, and Elena Marchiori.
Clustering metagenome short reads using weighted proteins.
In Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, 7th European Conference, EvoBIO 2009, Tübingen, Germany, April 15-17, 2009, Proceedings, volume 5483 of Lecture Notes in Computer Science, pages 152-163. Springer, 2009.

MLTreeMap 2.061 – Phylogenetics and Functionalities of Metagenomes

MLTreeMap 2.061

:: DESCRIPTION

MLTreeMap is a tool that employs full maximum likelihood to give insights into phylogenetic and functional properties of metagenomes and the underlying microbial communities. It does so by detecting and phylotyping a series of relevant marker genes on the submitted DNA fragments. Among these genes are protein coding phylogenetic markers, SSU rRNA genes and markers for important functional pathways.

::DEVELOPER

Christian von Mering (mering@imls.uzh.ch)

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • Blast
  • Gblocks

:: DOWNLOAD

 MLTreeMap

:: MORE INFORMATION

Citation

MLTreeMap–accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies.
Stark M, Berger SA, Stamatakis A, von Mering C.
BMC Genomics. 2010 Aug 5;11:461. doi: 10.1186/1471-2164-11-461.

ShotgunFunctionalizeR 1.2-9 – Functional Comparison of Metagenomes

ShotgunFunctionalizeR 1.2-9

:: DESCRIPTION

ShotgunFunctionalizeR is an R-package for functional comparison of metagenomes. The package contains tools for importing, annotating and visualising metagenomic data produced by shotgun high-throughput sequencing. ShotgunFunctionalizeR contains several statistical procedures for assessing functional differences between samples, both for individual genes and for entire pathways.

::DEVELOPER

Erik Kristiansson (erik.kristiansson@neuro.gu.se) , Daniel Dalevi (daniel.dalevi@gmail.com)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

   ShotgunFunctionalizeR

:: MORE INFORMATION

Citation

Kristiansson E, Hugenholtz P and Dalevi D. (2009).
ShotgunFunctionalizeR: An R-package for functional comparisons of metagenomes.
Bioinformatics. doi:10.1093/bioinformatics/btp508.

 

cBar 1.2 – Identification of Chromosomal Sequence Fragments from Metagenome data

cBar 1.2

:: DESCRIPTION

cBar is a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data

::DEVELOPER

the Computational Systems Biology Laboratory at the University of Georgia 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 cBar

:: MORE INFORMATION

Citation

Fengfeng Zhou, Ying Xu
cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data
Bioinformatics, 2010 26(16):2051-2052.

Treephyler 1.1 – Fast Taxonomic Profiling of Metagenomes.

Treephyler 1.1

:: DESCRIPTION

Treephyler is a tool for fast taxonomic profiling of metagenomes. It combines the predictive power of tree-based and speed of signature-based approaches. Treephyler was evaluated on a real metagenome to assess its performance in comparison to previous approaches for taxonomic profiling.

::DEVELOPER

Department of Bioinformatics ,  University of Göttingen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Treephyler

:: MORE INFORMATION

Citation

F. Schreiber, P. Gumrich , R. Daniel and P. Meinicke (2010)
Treephyler: fast taxonomic profiling of metagenomes
Bioinformatics 26, 960-961