Référentiel des outils installés sur la plateforme Migale
FASTX-Toolkit (version 0.0.13 - 2013-04-30)
The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences (possibly with quality information).
FigTree (version 1.4.0 - 2013-11-15)
FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. As with most of my programs, it was written for my own needs so may not be as polished and feature-complete as a commercial program. In particular it is designed to display summarized and annotated trees produced by BEAST.
Download : http://tree.bio.ed.ac.uk/software/figtree/
Usage : #figtree
FragGeneScan (version 1.30 - 2017-09-19)
FragGeneScan is an application for finding (fragmented) genes in short reads
Documentation : http://omics.informatics.indiana.edu/FragGeneScan/README
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])
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.
Documentation : https://github.com/ekg/freebayes#user-manual-and-guide
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
Documentation : http://genome.jouy.inra.fr/frost/frost_faq.shtml
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.
Download : http://appsrv.cse.cuhk.edu.hk/~tmchan/GALFP/
Documentation : http://appsrv.cse.cuhk.edu.hk/~tmchan/GALFP/
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.
Download : https://www.broadinstitute.org/gatk/download
Documentation : https://www.broadinstitute.org/gatk/guide/
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.
Documentation : http://algorithms.cnag.cat/wiki/GEM:Documentation