Référentiel des outils installés sur la plateforme Migale

MaxBin (version 2.2.1 - 2017-01-17)
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.
Usage : #run_MaxBin.pl -contig (contig file) -out (output file)

mcl (version 12-068 - 2013-08-22)
The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for networks (also known as graphs) based on simulation of (stochastic) flow in graphs.
Documentation : http://www.micans.org/mcl/
Usage : #mcl <-|file name> [options], do 'mcl -h' or 'man mcl' for help

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

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

miranda (version 3.3a - 2014-10-29)
miRanda is an algorithm for the detection of potential microRNA target sites in genomic sequences. miRanda reads RNA sequences (such as microRNAs) from file1 and genomic DNA/RNA sequences from file2. Both of these files should be in FASTA format.
Usage : #miranda file1 file2 [options..]


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by Dr. Radut