Référentiel des outils installés sur la plateforme Migale

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

FragGeneScan (version 1.30 - 2017-09-19)
FragGeneScan is an application for finding (fragmented) genes in short reads
Remarque : Demande faite suite à la suite de la réunion Tiagomics du 19/09/2017
Usage : #USAGE: run_FragGeneScan.pl -genome=[seq_file_name] -out=[output_file_name] -complete=[1 or 0] -train=[train_file_name] (-thread=[number of thread; default 1])

FragGeneScanPlusPlus (version la dernière ou la suivante tant qu'à faire - 2018-09-12)
FragGeneScan en ++ rapide Attention Véro, y a un petit défi pour l'installation, sinon c'est pas drôle
Usage : # FGS++ -s [seq_file_name] -m [max_mem_use] -o [output_file_name] -w [1 or 0] -t [train_file_name] -p [thread_num] -e [1 or 0] -d [1 or 0] FGS++ -s [seq_file_name] -m [max_mem_use] -o [output_file_name] -w [1 or 0] -t [train_file_name] -p [thread_num] -e [1 or 0] -d [1 or 0]

freebayes (version v1.1.0-1-gf15e66e - 2017-02-16)
FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.
Remarque : Citing freebayes:Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012
Usage : #freebayes -f [REFERENCE] [OPTIONS] [BAM FILES] >[OUTPUT]

frost (version 0.4.3 - 2002-05-01)
Outils de reconnaissance de repliement

GALF_P (version - - 2010-03-18)
GALF-P is a novel framework for TFBS identification (motif discovery) in DNA sequences. It consists of Genetic Algorithm with Local Filtering (GALF) and the post-processing procedure based on adaptive adding and removing. GALF-P achieves both effectiveness and efficiency, and provides reliable performance over the other state-of-art GA based approaches. The post-processing procedure is designed for zero or more TFBSs in each sequence.
Usage : #GALF_P.o

gatk (version - 2020-01-25)
The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyze high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Usage : #gatk --help

Gblocks (version 0.91b - 2006-07-19)
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis Gblocks eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences.
Usage : #Gblocks

GCTA (version 1.26.0 - 2017-09-15)
GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits. GCTA currently supports the analyses as follows.
Usage : #gcta64

GEM (version 20121106-022124 - 2013-07-25)
The GEM library(Also home to: The GEM mapper, The GEM RNA mapper, The GEM mappability, and others).Next-generation sequencing platforms (Illumina/Solexa, ABI/SOLiD, etc.) call for powerful and very optimized tools to index/analyze huge genomes. The GEM library strives to be a true "next-generation" tool for handling any kind of sequence data, offering state-of-the-art algorithms and data structures specifically tailored to this demanding task. At the moment, efficient indexing and searching algorithms based on the Burrows-Wheeler transform (BWT) have been implemented.

get_homologues (version 03012018 - 2018-01-24)
GET_HOMOLOGUES: a versatile software package for pan-genome analysis
Usage : #get_homologues.pl -h


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by Dr. Radut