Référentiel des outils installés sur la plateforme Migale


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 3.5 - 2016-01-25)
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 : #java -jar /usr/local/genome/gatk/GenomeAnalysisTK.jar -h



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.



HH-suite (version 2.0.16 - 2013-07-24)
The HH-suite is an open-source software package for highly sensitive sequence searching and sequence alignment. Its two most important programs are HHsearch and HHblits. Both are based on the pairwise comparison of pro file hidden Markov models (HMMs).



HISAT2 (version 2.0.4 - 2016-09-07)
HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads. In addition to one global FM index that represents a whole genome, HISAT uses a large set of small FM indexes that collectively cover the whole genome (each index represents a genomic region of ~64,000 bp and ~48,000 indexes are needed to cover the human genome). These small indexes (called local indexes) combined with several alignment strategies enable effective alignment of RNA-seq reads, in particular, reads spanning multiple exons. The memory footprint of HISAT is relatively low (~4.3GB for the human genome). We have developed HISAT based on the Bowtie2 implementation to handle most of the operations on the FM index.
Usage : #hisat2 [options]* -x {-1 -2 | -U | --sra-acc } [-S ]



hmmer (version 3.1 - 2013-08-23)
HMMER: profile HMMs for protein sequence analysis Profile hidden Markov models (profile HMMs) can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus.


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by Dr. Radut