Référentiel des outils installés sur la plateforme Migale
La liste des packages R installés sur la plateforme Migale est disponible ici.
IM-TORNADO (version 126.96.36.199 - 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.
Download : http://sourceforge.net/projects/imtornado
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
Download : http://www.iqtree.org
Documentation : http://www.iqtree.org/doc/iqtree-doc.pdf
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
Download : http://mcmc-jags.sourceforge.net/
Documentation : http://genome.jouy.inra.fr/doc/genome/calcul_numerique/
Usage : #jags
jalview (version 2.9.0 - 2016-03-10)
Jalview is a multiple alignment editor
Download : http://www.jalview.org/download.html
Documentation : http://www.jalview.org/help.html
Usage : #jalview
jellyfish (version 1.1.3 - 2011-12-21)
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism.JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command. See the documentation below for more details.
Documentation : http://genome.jouy.inra.fr/doc/genome/NGS/jellyfish-1.1.3/
Remarque : If you use JELLYFISH in your research, please cite: Guillaume Marcais and Carl Kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics (2011) 27(6): 764-770 (first published online January 7, 2011) doi:10.1093/bioinformatics/btr011
Usage : #jellyfish
Julia (version 0.5.0 - 2017-02-08)
Julia is a high-level, high-performance dynamic programming language fortechnical computing, with syntax that is familiar to users of other technicalcomputing environments.It is a very performant programming language somehow similar to R, Matlab orPython, but with performances approaching those of C/Fortran.
Download : http://julialang.org/
Documentation : http://docs.julialang.org/en/stable/#manual
Usage : #julia
kaiju (version 1.6.0 - 2018-01-16)
Kaiju is a program for the taxonomic classification of metagenomic high-throughput sequencing reads. Each read is directly assigned to a taxon within the NCBI taxonomy by comparing it to a reference database containing microbial and viral protein sequences.
Remarque : CitationMenzel P., Ng K.L., Krogh A. (2016) Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat. Commun. 7:11257
Usage : #kaiju -t nodes.dmp -f kaiju_db.fmi -i reads.fastq [-j reads2.fastq]
kraken (version 0.10.5 - 2015-11-25)
raken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.
Documentation : http://ccb.jhu.edu/software/kraken/MANUAL.html
Remarque : If you use Kraken in your research, please cite our paper; the citationis available on the Kraken website.
Usage : #kraken [options]
kSNP (version 2.1.2 - 2014-04-24)
Indentify SNPs in a set of genome sequences without the requirement of a reference sequence or a multiple sequence alignment.Reconstruction of SNP based phylogenies by maximum likelihood.
Download : http://sourceforge.net/projects/ksnp/
Usage : #kSNP -k kmer_length -f fasta -d output_directory [-p genomes4positions_list] [-u unassembled_genomes_list] [-m minimum_fraction_genomes_with_locus] [-G genbank.gbk] [-n num_CPU] [-j ] [-v ] [-c min_kmer_coverage]