Référentiel des outils installés sur la plateforme Migale

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

Megahit (version 1.0.4-beta - 2016-03-17)
MEGAHIT: An ultra-fast single-node solution for large and complexmetagenomics assembly via succinct de Bruijn graph
Usage : # megahit [options] {-1 -2 | --12 | -r } [-o ]

megan (version 5.10.6 - 2015-07-12)
MEGAN - Metagenome Analysis Software
Usage : #megan

MeShClust (version la plus récente de préférence, parce que sinon on n'est pas à jour - 2018-05-18)
MeShClust: an intelligent tool for clustering DNA sequences
Usage : #meshclust *.fasta [--id 0.90] [--kmer 3] [--delta 5] [--output output.clstr] [--iterations 20] [--align] [--sample 1500] [--pivot 40] [--threads TMAX]

metabat2 (version 2.12.1 - 2019-07-31)
MetaBAT: A robust statistical framework for reconstructing genomes from metagenomic data
Usage : #metabat2 -h

MetaOthello (version 1.0 - 2018-05-23)
A Novel Data Structure to Support Ultra-fast Taxonomic Classification of Metagenomic Sequences with k-mer Signatures

mga (version none - 2014-11-20)
Multiple Genome Aligner (MGA for short) computes multiple genome alignments of large, closely related DNA sequences.
Usage : #mga

mgltools (version 1.5.6 - 2015-03-11)
MGLTools is a software developed at the Molecular Graphics Laboratory (MGL) of The Scripps Research Institute for visualization and analysis of molecular structures. Short description and demo of its three main applications are given below. Navigation portlet on the left has links to downloads, screenshots, documentation section of this website where you can find more information about MGLTools. Please visit MGL Bugzilla to submit a bug report or to request a new feature.
Usage : #pmv, adt, vision

micca (version 1.5.0 - 2017-02-27)
micca (MICrobial Community Analysis) is a software pipeline for theprocessing of amplicon sequencing data, from raw sequences to OTU tables,taxonomy classification and phylogenetic tree inference. The pipeline can beapplied to a range of highly conserved genes/spacers, such as 16S rRNA gene,Internal Transcribed Spacer (ITS) and 28S rRNA.
Usage : #micca [--version] [--help] []

minia (version 1.4683 - 2013-02-21)
Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. The output of Minia is a set of contigs. Minia produces results of similar contiguity and accuracy to other de Bruijn assemblers (e.g. Velvet).
Remarque : PDF and CitationR. Chikhi, G. Rizk. Space-efficient and exact de Bruijn graph representation based on a Bloom filter, WABI 2012
Usage : #minia fasta_file kmer_size min_abundance estimated_genome_size prefix

mira (version 4.0 - 2014-11-18)
MIRA is a Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina. It can perform Hybrid de-novo assemblies as well as SNP and mutations discovery for mapping assemblies.
Usage : #mira


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by Dr. Radut