MAIRA 0.1.7 – Real-time Taxonomic and Functional analysis of long Reads on a laptop

MAIRA 0.1.7

:: DESCRIPTION

MAIRA is a new standalone program for interactive taxonomic and functional analysis of long read metagenomic sequencing data on a laptop without internet access. The program performs fast, online, genus-level analysis, and on-demand, detailed taxonomic and functional analysis. It uses two levels of frame-shift-aware alignment of DNA reads against protein reference sequences, and then performs detailed analysis using a protein synteny graph.

::DEVELOPER

the Algorithms in Bioinformatics lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

MAIRA

:: MORE INFORMATION

Citation

Albrecht B, Bağcı C, Huson DH.
MAIRA- real-time taxonomic and functional analysis of long reads on a laptop.
BMC Bioinformatics. 2020 Sep 17;21(Suppl 13):390. doi: 10.1186/s12859-020-03684-2. PMID: 32938391; PMCID: PMC7495841.

Microtaxi – Microbial Taxonomic Identification and Classification Server

Microtaxi

:: DESCRIPTION

Microtaxi uses an taxon-specific gene based approach and provides an alternate valuable methodology to carry out the taxonomic classification of newly sequenced or existing bacterial genomes.

::DEVELOPER

MetaBioSys laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 Microtaxi

:: MORE INFORMATION

Citation

BMC Genomics. 2015 May 20;16:396. doi: 10.1186/s12864-015-1542-0.
Using the taxon-specific genes for the taxonomic classification of bacterial genomes.
Gupta A, Sharma VK

FishTaco 1.1.3 – Linking Taxonomic and Functional Shifts in the Microbiome

FishTaco 1.1.3

:: DESCRIPTION

FishTaco (Functional Shifts Taxonomic Contributors) is a metagenomic computational framework, aiming to identify the taxa that are driving the functional shifts we observe in microbiomes of different individuals or disease states.

::DEVELOPER

the Borenstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

FishTaco

:: MORE INFORMATION

Citation

Cell Host Microbe. 2017 Feb 8;21(2):254-267. doi: 10.1016/j.chom.2016.12.014.
Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome.
Manor O, Borenstein E.

Kraken 1.1.1 – Kraken Taxonomic Sequence Classification System

Kraken 1.1.1

:: DESCRIPTION

Kraken is a very fast system for taxonomic classification of short or long DNA sequences from a microbiome or metagenomic sample.

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 Kraken

:: MORE INFORMATION

Citation

Genome Biol. 2014 Mar 3;15(3):R46. doi: 10.1186/gb-2014-15-3-r46.
Kraken: ultrafast metagenomic sequence classification using exact alignments.
Wood DE, Salzberg SL.

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