Référentiel des outils installés sur la plateforme Migale
La liste des packages R installés sur la plateforme Migale est disponible ici.
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]
kraken2 (version 2.0 - 2018-09-06)
The second version of the Kraken taxonomic sequence classification system
Documentation : http://ccb.jhu.edu/software/kraken/
Usage : #kraken2 [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]
LoRDEC (version 0.7 - 2017-11-03)
LoRDEC: a hybrid error correction program for long, PacBio reads LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads. It uses a hybrid strategy, meaning that it uses two sets of reads: the reference read set, whose error rate is assumed to be small, and the PacBio read set, which is then corrected using the reference set. Typically, the reference set contains Illumina reads.
Remarque : L. Salmela and E. Rivals LoRDEC: accurate and efficient long read error correction Bioinformatics 30(24):3506-3514, 2014, doi: 10.1093/bioinformatics/btu538.
Usage : #lordec-correct [-t
] [-b ] [-e ] [-T ] [-S ] [-c] -i -2 -k -o
macsyfinder (version 1.5.0 - 2018-03-23)
Detection of macromolecular systems in protein datasets using systems modelling and similarity search.
Download : https://github.com/gem-pasteur/macsyfinder
Usage : #macsyfinder_env
mafft (version 7.310 - 2017-08-28)
MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods.
Usage : #mafft [options] input > output
Mash (version 2.0 - 2018-01-29)
Fast genome and metagenome distance estimation using MinHash
Download : https://github.com/marbl/Mash
Documentation : https://github.com/marbl/Mash
Remarque : Mash: fast genome and metagenome distance estimation using MinHash. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. Genome Biol. 2016 Jun 20;17(1):132. doi: 10.1186/s13059-016-0997-x.
Usage : #mash
[options] [arguments ...]
mauve (version 2.4.0 - 2015-01-07)
Multiple Alignment of Conserved Regions in Genome Sequences
Download : http://gel.ahabs.wisc.edu/mauve/download.php
Documentation : http://darlinglab.org/mauve/user-guide/overview.html
Usage : #mauve
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.
Download : http://www.micans.org/mcl/src/
Documentation : http://www.micans.org/mcl/
Usage : #mcl <-|file name> [options], do 'mcl -h' or 'man mcl' for help