Elviz 2.0 – Exploration of Metagenomic Assemblies

Elviz 2.0

:: DESCRIPTION

Elviz (Environmental Laboratory Visualization) is an interactive web-based tool for the visual exploration of assembled metagenome data and their complex metadata.

:: DEVELOPER

Joint Genome Institute (JGI).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Elviz – exploration of metagenome assemblies with an interactive visualization tool.
Cantor M, Nordberg H, Smirnova T, Hess M, Tringe S, Dubchak I.
BMC Bioinformatics. 2015 Apr 28;16(1):130.

MetAMOS 1.5rc3 – Metagenomic Assembly pipeline for AMOS

MetAMOS 1.5rc3

:: DESCRIPTION

MetAMOS is an open source and modular metagenomic assembly and analysis pipeline. MetAMOS represents an important step towards fully automated metagenomic analysis, starting with next-generation sequencing reads and producing genomic scaffolds, open-reading frames and taxonomic or functional annotations.

::DEVELOPER

Treangen Lab

:: SCREENSHOTS

:: REQUIREMENTS

Linux
Java
Perl

:: DOWNLOAD

MetAMOS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 May 3;15:126. doi: 10.1186/1471-2105-15-126.
Automated ensemble assembly and validation of microbial genomes.
Koren S1, Treangen TJ, Hill CM, Pop M, Phillippy AM.

Genome Biol. 2013 Jan 15;14(1):R2.
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline.
Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M.

InteMAP 1.0 – Integrated Metagenomic Assembly pipeline for NGS Short Reads

InteMAP 1.0

:: DESCRIPTION

InteMAP is a pipeline which integrates individual assemblers for assembling metagenomic short sequencing reads.

::DEVELOPER

ZhuLab, Peking Uiniversity, Beijing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

InteMAP

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2015 Aug 7;16:244. doi: 10.1186/s12859-015-0686-x.
InteMAP: Integrated metagenomic assembly pipeline for NGS short reads.
Lai B, Wang F, Wang X, Duan L, Zhu H

MAP 20121108 – A de novo Metagenomic Assembly program for Shotgun DNA reads

MAP 20121108

:: DESCRIPTION

MAP (Metagenomic Assembly program) is a de novo assembly approach and its implementation based on an improved Overlap/Layout/Consensus (OLC) strategy incorporated with several special algorithms.MAP uses the mate pair information, resulting in being more applicable to shotgun DNA reads (recommended as > 200 bp) currently widely-used in metagenome projects. Results of extensive tests on simulated data show that MAP can be superior to both Celera and Phrap for typical longer reads by Sanger sequencing, as well as has an evident advantage over Celera, Newbler, and the newest Genovo, for typical shorter reads by 454 sequencing.

::DEVELOPER

ZhuLab, Peking Uiniversity, Beijing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

MAP

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jun 1;28(11):1455-62. Epub 2012 Apr 11.
A de novo metagenomic assembly program for shotgun DNA reads.
Lai B, Ding R, Li Y, Duan L, Zhu H.