Référentiel des outils installés sur la plateforme Migale

La liste des packages R installés sur la plateforme Migale est disponible ici.

Git lfs (version 2.4.2 - 2018-06-11)
Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com or GitHub Enterprise.
Usage : #git-lfs []

HH-suite (version 2.0.16 - 2013-07-24)
The HH-suite is an open-source software package for highly sensitive sequence searching and sequence alignment. Its two most important programs are HHsearch and HHblits. Both are based on the pairwise comparison of pro file hidden Markov models (HMMs).

HISAT2 (version 2.0.4 - 2016-09-07)
HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads. In addition to one global FM index that represents a whole genome, HISAT uses a large set of small FM indexes that collectively cover the whole genome (each index represents a genomic region of ~64,000 bp and ~48,000 indexes are needed to cover the human genome). These small indexes (called local indexes) combined with several alignment strategies enable effective alignment of RNA-seq reads, in particular, reads spanning multiple exons. The memory footprint of HISAT is relatively low (~4.3GB for the human genome). We have developed HISAT based on the Bowtie2 implementation to handle most of the operations on the FM index.
Usage : #hisat2 [options]* -x {-1 -2 | -U | --sra-acc } [-S ]

hmmer (version 3.2.1 - 2019-01-22)
HMMER: profile HMMs for protein sequence analysis Profile hidden Markov models (profile HMMs) can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus.
Usage : #hmmsearch [options]

i-ADHoRe (version 3.0.01 - 2013-10-30)
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, theimplementation 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 genomicsegments 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.
Usage : #i-adhore

igv (version 2.3.67 - 2016-01-11)
The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
Remarque : To cite your use of IGV in your publication:James T. Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S. Lander, Gad Getz, Jill P. Mesirov. Integrative Genomics Viewer. Nature Biotechnology 29, 24–26 (2011)
Usage : #igv

IM-TORNADO (version - 2016-02-22)
Illumina paired-end sequencing, which produces two separate reads for eachDNA fragment, has become the platform of choice for 16S rDNA hypervariabletag sequencing. However, when the two reads do not overlap, existingcomputational pipelines analyze data from read separately and underutilizethe information contained in the paired-end reads. IM-TORNADO is a tool forprocessing non-overlapping reads while retaining maximal information content.
Remarque : If you use IM-TORNADO for your project, please cite the following manuscript:Jeraldo P, Kalari K, Chen X, Bhavsar J, Mangalam A, White B, et al. IM-TORNADO: A Tool for Comparison of 16S Reads from Paired-End Libraries. PLOS ONE 9 (12):e114804. Available from: http://dx.plos.org/10.1371/journal.pone.0114804

Insyght (version - 2014-01-01)
Insyght is genomic visualisation tool that combines a symbolic and a proportional view of the genes, syntenies and genomic regions. Another of Insyght's feature is synchronized navigation and zooming across multiple species.

IQ-TREE (version 1.6.1 - 2018-01-12)
Efficient software for phylogenomic inference
Usage : #iqtree -h

JAGS (version 3.4.0 - 2013-12-17)
JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS. JAGS was written with three aims in mind: To have a cross-platform engine for the BUGS language To be extensible, allowing users to write their own functions, distributions and samplers. To be a plaftorm for experimentation with ideas in Bayesian modelling
Usage : #jags


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