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.

Divers


VersionMAJ

bedtools

2.16.22012-10-09DownloadDoc
The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by "streaming" several BEDTools together. The following are examples of common questions that one can address with BEDTools.

Remarque Please cite the following article if you use BEDTools in your research: Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842.
Run Unix # Run Web #

VersionMAJ

i-ADHoRe

3.0.012013-10-30DownloadDoc
This novel version of i-ADHoRe is designed to detect genomic homology in extremely large-scale data sets. Along with several under-the hood-improvements, resulting in a 30 fold reduction in runtime over previous versions, the implementation of multithreading and MPI now enables i-ADHoRe to take advantage of a parallel computing platform. As the scale of the data sets increased, the need for a new alignment algorithm able to cope with dozens of genomic segments became apparent. Therefore a new greedy graph based alignment algorithm has been implemented (described in Fostier et al., 2011), allowing analysis of even the largest data sets currently available.

Remarque
Run Unix # i-adhoreRun Web #

VersionMAJ

pandoc

1.9.4.12016-02-23DownloadDoc
Pandoc is a free and open-source software document converter, widely used as a writing tool and as a basis for publishing workflows. Pandoc can convert documents in markdown, reStructuredText, textile, HTML, DocBook, LaTeX, MediaWiki markup, TWiki markup, OPML, Emacs Org-Mode, Txt2Tags, Microsoft Word docx, LibreOffice ODT, EPUB, or Haddock markup to HTML formats: XHTML, HTML5, and HTML slide shows using Slidy, reveal.js, Slideous, S5, or DZSlides. Word processor formats: Microsoft Word docx, OpenOffice/LibreOffice ODT, OpenDocument XML Ebooks: EPUB version 2 or 3, FictionBook2 Documentation formats: DocBook, GNU TexInfo, Groff man pages, Haddock markup Page layout formats: InDesign ICML Outline formats: OPML TeX formats: LaTeX, ConTeXt, LaTeX Beamer slides PDF via LaTeX Lightweight markup formats: Markdown (including CommonMark), reStructuredText, AsciiDoc, MediaWiki markup, DokuWiki markup, Emacs Org-Mode, Textile Custom formats: custom writers can be written in lua.

Remarque
Run Unix # pandoc [OPTIONS] [FILES] Run Web #

VersionMAJ

qpdf

5.1.32015-08-26DownloadDoc
QPDF is a command-line program that does structural, content-preserving transformations on PDF files. It could have been called something like pdf-to-pdf. It also provides many useful capabilities to developers of PDF-producing software or for people who just want to look at the innards of a PDF file to learn more about how they work.

Remarque
Run Unix # qpdf [options] infile outfileRun Web #

VersionMAJ

quantiNemo

1.0.42015-02-24DownloadDoc
quantiNEMO is an individual-based, genetically explicit stochastic simulation program. It was developed to investigate the effects of selection, mutation, recombination, and drift on quantitative traits with varying architectures in structured populations connected by migration and located in a heterogeneous habitat. quantiNEMO is highly flexible at various levels: population, selection, trait(s) architecture, genetic map for QTL and/or markers, environment, demography, mating system, etc.

Remarque
Run Unix # quantiNemoRun Web #

VersionMAJ

riboPicker

0.4.32013-07-29DownloadDoc
Easy identification and removal of rRNA-like sequences. The riboPicker tool can be used to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface.

Remarque
Run Unix # ribopicker [options] -f -dbs ...Run Web #

VersionMAJ

SortMeRNA

1.92014-02-20DownloadDoc
SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. It is capable of handling large RNA databases and sorting out all fragments matching to the database with high accuracy and specificity.

Remarque If you use SortMeRNA, please cite: Kopylova E., Noé L. and Touzet H., "SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data", Bioinformatics (2012), doi: 10.1093/bioinformatics/bts611.
Run Unix # sortmerna -h Run Web #

VersionMAJ

SPiD

2.1DownloadDoc
Subtilis Protein interaction Database

Remarque
Run Unix # Run Web # http://genome.jouy.inra.fr/cgi-bin/spid/index.cgi

VersionMAJ

SRA ToolKit

2.5.72016-01-30DownloadDoc
The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format (Note that this is not required for submission). The Toolkit source code is provided in the form of the SRA SDK, and may be compiled with GCC. However, pre-built software executables are available for Linux, Windows, and Mac OS X, and we highly recommend using these pre-built executables whenever possible.

Remarque
Run Unix # Run Web #

Menu principal

Page | by Dr. Radut