iVikodak – A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets

iVikodak

:: DESCRIPTION

iVikodak (a word derived from Sanskrit language, which refers to ‘Decoder’) is a multi-modular web-platform that hosts a logically inter-connected repertoire of functional inference and analysis tools, coupled with a comprehensive visualization interface.

::DEVELOPER

iVikodak team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

WEb browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Nagpal S, Haque MM, Singh R, Mande SS.
iVikodak-A Platform and Standard Workflow for Inferring, Analyzing, Comparing, and Visualizing the Functional Potential of Microbial Communities.
Front Microbiol. 2019 Jan 14;9:3336. doi: 10.3389/fmicb.2018.03336. PMID: 30692979; PMCID: PMC6339920.

Vikodak – A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets.
Nagpal S, Haque MM, Mande SS.
PLoS One. 2016 Feb 5;11(2):e0148347. doi: 10.1371/journal.pone.0148347.

TagCleaner 0.16 – Detect and Remove Tag Sequences from Metagenomic datasets

TagCleaner 0.16

:: DESCRIPTION

TagCleaner is a tool to automatically detect and efficiently remove tag sequences (e.g. WTA or MID tags) from metagenomic datasets.

TagCleaner Online Version

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Mac OsX / Linux /
Perl

:: DOWNLOAD

TagCleaner

:: MORE INFORMATION

Citation:

Schmieder R, Lim YW, Rohwer F, Edwards R
TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets.
BMC Bioinformatics 2010, 11:341.

DeconSeq 0.4.3 – Detect and Remove Contaminations from Metagenomic datasets

DeconSeq 0.4.3

:: DESCRIPTION

DeconSeq is a tool to automatically detect and efficiently remove any type of known sequence contamination from metagenomic datasets. The tool uses a modified version of the BWA-SW aligner and can be applied to longer-read datasets (150+bp read length).

DeconSeq Online Version

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Mac OsX / Linux /
Perl

:: DOWNLOAD

DeconSeq

:: MORE INFORMATION

Citation:

Schmieder R and Edwards R
Fast identification and removal of sequence contamination from genomic and metagenomic datasets.
PLoS ONE 2011, 6:e17288

Genometa 0.51 – Rapid Analysis of Metagenomic Datasets

Genometa 0.51

:: DESCRIPTION

Genometa is a Java based local bioinformatics program which allows rapid analysis of metagenomic short read datasets. Millions of short reads can be accurately analysed within minutes and visualised in the browser component. A large database of diverse bacteria and archaea has been constructed as a reference sequence.

::DEVELOPER

Genometa Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / MacOsX
Java

:: DOWNLOAD

Genometa

:: MORE INFORMATION

Citation

PLoS One. 2012;7(8):e41224. doi: 10.1371/journal.pone.0041224. Epub 2012 Aug 21.
Genometa–a fast and accurate classifier for short metagenomic shotgun reads.
Davenport CF, Neugebauer J, Beckmann N, Friedrich B, Kameri B, Kokott S, Paetow M, Siekmann B, Wieding-Drewes M, Wienhöfer M, Wolf S, Tümmler B, Ahlers V, Sprengel F.