MOCAT2 2.0 – Analyzing Metagenomics Datasets

MOCAT2 2.0

:: DESCRIPTION

MOCAT (Metagenomics Analysis Toolkit) is a package for analyzing metagenomics datasets. Currently MOCAT supports Illumina single- and paired-end reads in raw FastQ format. Using MOCAT you can, for example, generate taxonomic profiles of, and assemble, metagenomes.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

MOCAT

:: MORE INFORMATION

Citation:

MOCAT2: a metagenomic assembly, annotation and profiling framework.
Kultima JR, Coelho LP, Forslund K, Huerta-Cepas J, Li SS, Driessen M, Voigt AY, Zeller G, Sunagawa S, Bork P.
Bioinformatics. 2016 Aug 15;32(16):2520-3. doi: 10.1093/bioinformatics/btw183.

PLoS One. 2012;7(10):e47656. doi: 10.1371/journal.pone.0047656. Epub 2012 Oct 17.
MOCAT: a metagenomics assembly and gene prediction toolkit.
Kultima JR, Sunagawa S, Li J, Chen W, Chen H, Mende DR, Arumugam M, Pan Q, Liu B, Qin J, Wang J, Bork P.

FMAP – Functional Mapping and Analysis Pipeline for Metagenomics and Metatranscriptomics studies

FMAP

:: DESCRIPTION

FMAP (Functional Mapping and Analysis Pipeline) is an open-sourced, stand-alone functional analysis pipeline for analyzing whole metagenomic and metatranscriptomic sequencing data.

::DEVELOPER

The Quantitative Biomedical Research Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
Perl

:: DOWNLOAD

FMAP

:: MORE INFORMATION

Citation

Kim J, Kim MS, Koh AY, Xie Y, Zhan X.
FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies
BMC Bioinformatics. 2016 Oct 10;17(1):420.PMID: 27724866

Metarep 1.4.0 – High-performance Comparative Metagenomics Tool

Metarep 1.4.0

:: DESCRIPTION

METAREP (JCVI Metagenomics Reports) is a new open source tool for high-performance comparative metagenomics. It provides a suite of web based tools to help scientists to view, query, browse and compare metagenomics annotation data derived from ORFs called on metagenomics reads.

METAREP supports browsing of functional and taxonomic assignments. Users can either specify fields, or logical combinations of fields to flexibly filter datasets on the fly. Users can compare multiple datasets at various functional and taxonomic levels applying statistical tests as well as hierarchical clustering, multidimensional scaling and heatmaps.

::DEVELOPER

J. Craig Venter Institute

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Metarep

:: MORE INFORMATION

Citation:

Johannes Goll etc.
METAREP: JCVI metagenomics reports—an open source tool for high-performance comparative metagenomics
Bioinformatics (2010) 26 (20): 2631-2632.