PHYLOSHOP 1.01 – Predicts 16S rRNA Gene Fragments in Metagenomes

PHYLOSHOP 1.01

:: DESCRIPTION

PHYLOSHOP is a pipeline that predicts 16S rRNA gene fragments in metagenomes, reports the taxonomic assignment of these fragments, and visualizes their taxonomy distribution.

::DEVELOPER

Yuzhen Ye lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 PHYLOSHOP

:: MORE INFORMATION

Citation:

Neethu Shah, Haixu Tang, Thomas G. Doak and Yuzhen Ye.
Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics.
Pac Symp Biocomput. p:165-76 (2011)

MetaTISA – Translation Initiation Site Annotation for Metagenomes

MetaTISA

:: DESCRIPTION

MetaTISA is tool with an aim to improve translationa initiation sites (TISs) prediction of current gene-finders for metagenomes. The method employs a two-step strategy to predict TISs by first clustering metagenomic fragments into phylogenetic groups and then predicting TISs independently for each group in an unsupervised manner. As evaluated on experimentally verified TISs, MetaTISA greatly improves the accuracies of TIS prediction of current gene-finders.

::DEVELOPER

ZhuLab, Peking Uiniversity, Beijing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 MetaTISA

:: MORE INFORMATION

Citation

Gang-Qing Hu, Jiang-Tao Guo, Yong-Chu Liu, and Huaiqiu Zhu.
MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction.
Bioinformatics 2009,25(14):1843-1845.

MEGAN 6.4.8 – Metagenome analysis

MEGAN 6.4.8

:: DESCRIPTION

MEGAN (MEta Genome ANalyzer) allows laptop analysis of large metagenomic data sets. In a preprocessing step, the set of DNA sequences is compared against databases of known sequences using BLAST or another comparison tool. MEGAN is then used to compute and explore the taxonomical content of the data set, employing the NCBI taxonomy to summarize and order the results. A simple lowest common ancestor algorithm assigns reads to taxa such that the taxonomical level of the assigned taxon reflects the level of conservation of the sequence. The software allows large data sets to be dissected without the need for assembly or the targeting of specific phylogenetic markers. It provides graphical and statistical output for comparing different data sets.

::DEVELOPER

Daniel Huson’s Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

 MEGAN

:: MORE INFORMATION

Citation

Analysis of 16S rRNA environmental sequences using MEGAN.
Mitra S, Stärk M, Huson DH.
BMC Genomics. 2011 Nov 30;12 Suppl 3:S17. doi: 10.1186/1471-2164-12-S3-S17.

FOCUS 0.29 – A model to Identify Organisms present in Metagenomes

FOCUS 0.29

:: DESCRIPTION

FOCUS, an innovative and agile composition based using non-negative least squares to profile and report abundant organisms present in me-tagenomic samples and their relative abundance without sequence length dependencies.

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX / Linux
  • Python

:: DOWNLOAD

 FOCUS

:: MORE INFORMATION

Citation:

Silva, G. G. Z., D. A. Cuevas, B. E. Dutilh, and R. A. Edwards, 2014
FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares.
PeerJ, 2, e425, doi:10.7717/peerj.425.

PyroTrimmer 1.1 – Preprocessor of Metagenome Sequences

PyroTrimmer 1.1

:: DESCRIPTION

PyroTrimmer is a program that trims barcodes, linkers, primers, and sequence region with low quality scores from 454 sequence reads.

::DEVELOPER

PyroTrimmer team

:: SCREENSHOTS

PyroTrimmer

:: REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

 PyroTrimmer

:: MORE INFORMATION

Citation

J Microbiol. 2012 Oct;50(5):766-9. doi: 10.1007/s12275-012-2494-6.
PyroTrimmer: a software with GUI for pre-processing 454 amplicon sequences.
Oh J1, Kim BK, Cho WS, Hong SG, Kim KM.

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.

FCMM 2.0.0 – Functional Characterization of Multiple Metagenome samples

FCMM 2.0.0

:: DESCRIPTION

FCMM is a pipeline for top-k based functional characterization of multiple metagenome samples to infer the major functions as well as their quantitative scores in a comparative metagenomics manner.

::DEVELOPER

the Bioinformatics Laboratory,Konkuk University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • awk (GNU awk 3.1.7)
  • sed (GNU sed 4.2.1)
  • BWA (v0.7.10)
  • DIAMOND (v0.7.8.57)
  • Trimmomatic (v0.33)

:: DOWNLOAD

 FCMM

:: MORE INFORMATION

Citation

FCMM: A comparative metagenomic approach for functional characterization of multiple metagenome samples.
Lee J, Lee HT, Hong WY, Jang E, Kim J.
J Microbiol Methods. 2015 Aug;115:121-8. doi: 10.1016/j.mimet.2015.05.023

SEAStAR v0.4.18 – Analysis of Next-generation Metagenomes

SEAStAR v0.4.18

:: DESCRIPTION

SEAStAR is a package of open-source tools supporting the construction of analysis pipelines for environmental next-generation sequencing data.

::DEVELOPER

Armbrust Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 SEAStAR

:: MORE INFORMATION

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)