Référentiel des outils installés sur la plateforme Migale

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

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.
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
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
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.
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

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]


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