Arrêt de l'ensemble des services de la plateforme Migale à partir du lundi 3 avril 2017

La plateforme Migale sera indisponible du 3 au 10 avril 2017. Cette indisponibilité est dûe à l'arrêt du DataCenter Ile-de-France qui héberge l'infrastructure de la plateforme.

Merci d'avance de votre compréhension.

Pour toutes questions ou informations supplémentaires, merci de contacter help.migale@jouy.inra.fr.

Analyse de métagénomes


VersionMAJ

FROGS

0.0.6DownloadDoc
Find Rapidly OTUs with Galaxy Solution: FROGS is a galaxy/CLI workflow designed to produce an OTU count matrix from high depth sequencing amplicon data. This workflow is focused on: - User-friendliness with the integration in galaxy and lots of rich graphic outputs - Accuracy with a clustering without global similarity threshold, the management of multi-affiliations and management of separated PCRs in the chimera removal step - Speed with fast algorithms and an easy to use parallelisation - Scalability with algorithms designed to support the data growth

Remarque
Run Unix # Run Web #

VersionMAJ

MaxBin

2.2.1 2017-01-17DownloadDoc
MaxBin is a software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Users could understand the underlying bins (genomes) of the microbes in their metagenomes by simply providing assembled metagenomic sequences and the reads coverage information or sequencing reads. For users' convenience MaxBin will report genome-related statistics, including estimated completeness, GC content and genome size in the binning summary page. Users could use MEGAN or similar software on MaxBin bins to find out the taxonomy of each bin after the binning process is finished.

Remarque
Run Unix # run_MaxBin.pl -contig (contig file) -out (output file) Run Web #

VersionMAJ

megan

5.10.62015-07-12DownloadDoc
MEGAN - Metagenome Analysis Software

Remarque
Run Unix # meganRun Web #

VersionMAJ

MetaSim

0.9.52010-09-28DownloadDoc
MetaSim - A Sequencing Simulator for Genomics and Metagenomics

Remarque f you use this program for your own research please cite our software. Publication: Richter DC, Ott F, Auch AF, Schmid R, Huson DH (2008) MetaSim—A Sequencing Simulator for Genomics and Metagenomics. PLoS ONE 3(10): e3373. doi:10.1371/journal.pone.0003373
Run Unix # MetaSimRun Web #

VersionMAJ

micca

1.5.02017-02-27DownloadDoc
micca (MICrobial Community Analysis) is a software pipeline for the processing of amplicon sequencing data, from raw sequences to OTU tables, taxonomy classification and phylogenetic tree inference. The pipeline can be applied to a range of highly conserved genes/spacers, such as 16S rRNA gene, Internal Transcribed Spacer (ITS) and 28S rRNA.

Remarque
Run Unix # micca [--version] [--help] [] Run Web #

VersionMAJ

MOCAT

1.12012-08-01DownloadDoc
MOCAT is a package for analyzing metagenomics datasets. Currently MOCAT supports Illumina single- and paired-end reads in raw FastQ format.

Remarque Jens Roat Kultima & Shinichi Sunagawa (Bork Group, EMBL)
Run Unix # MOCAT.pl -sf|sample_file 'FILE' [Pipeline, Statistics, & Additional Options]Run Web #

VersionMAJ

qiime

1.9.12016-11-14DownloadDoc
QIIME (pronounced "chime") stands for Quantitative Insights Into Microbial Ecology. QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data). QIIME takes users from their raw sequencing output through initial analyses such as OTU picking, taxonomic assignment, and construction of phylogenetic trees from representative sequences of OTUs, and through downstream statistical analysis, visualization, and production of publication-quality graphics. QIIME has been applied to single studies based on billions of sequences from thousands of samples.

Remarque
Run Unix # qiime_envRun Web #

VersionMAJ

SUPER-FOCUS

0.262016-10-04DownloadDoc
SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reduced SEED database to report the subsystems present in metagenomic samples and profile their abundances. The tool was tested with over 70 real metagenomes, and the results show that our approach accurately predicts the subsystems present in microbial communities, and it can be up to over 1,000 times faster than other tools.

Remarque
Run Unix # Run Web #

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