Référentiel des outils installés sur la plateforme Migale
EDGE-pro (version 1.3.1 - 2013-07-02)
EDGE-pro, Estimated Degree of Gene Expression in PROkaryots is an efficient software system to estimate gene expression levels in prokaryotic genomes from RNA-seq data. EDGE-pro uses Bowtie2 for alignment and then estimates expression directly from the alignment results.EDGE-pro includes routines to assign reads aligning to overlapping gene regions accurately. 15% or more of bacterial genes overlap other genes, making this a significant problem for bacterial RNA-seq, one that is generally ignored by programs designed for eukaryotic RNA-seq experiments.
Documentation : http://genome.jouy.inra.fr/doc/genome/NGS/EDGE-pro-1.3.1/
Remarque : Please reference our paper:T. Magoc, D. Wood, and S.L. Salzberg. EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes. Evolutionary Bioinformatics vol.9, pp.127-136, 2013.
Usage : #edge.pl <-g genome> <-p ptt> <-r rnt> <-u reads>
eggnog-mapper (version 0.99.3 - 2017-07-13)
eggnog-mapper is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments. Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs. The use of orthology predictions for functional annotation is considered more precise than traditional homology searches, as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence).
Documentation : https://github.com/jhcepas/eggnog-mapper/wiki
Remarque : Merci d'avance, cordialement
Usage : #emapper.py [-h]
emboss (version 184.108.40.206 - 2013-08-19)
Within EMBOSS you will find around 100 programs (applications). These are just some of the areas covered (Sequence alignment, Rapid database searching with sequence patterns,Protein motif identification, including domain analysis, Nucleotide sequence pattern analysis, for example to identify CpG islands or repeats, Codon usage analysis for small genomes, Rapid identification of sequence patterns in large scale sequence sets, Presentation tools for publication...)
Download : http://emboss.sourceforge.net/download/
fasta (version 3.6 - 2014-02-21)
A set of sequence comparison tools (fasta36, ggsearch...) used for alignment and database searching.For example, fasta compares a protein sequence to another protein sequence or to a protein database, or a DNA sequence to another DNA sequence or a DNA library.
Documentation : http://fasta.bioch.virginia.edu/fasta_www2/fasta_intro.shtml
Usage : #fasta36
FastQC (version 0.10.0 - 2012-03-05)
FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.
Documentation : http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/Help/
Usage : #fastqc ou fastqc seqfile1 seqfile2 .. seqfileN
fastqp (version 0.1.9.1 - 2017-02-27)
Simple FASTQ, SAM and BAM read quality assessment and plotting using Python.
Download : https://github.com/mdshw5/fastqp
Documentation : https://github.com/mdshw5/fastqp
Usage : #fastqp [-h]
Fastq_Screen (version 0.4.4 - 2014-07-09)
Fastq screen is a simple application which allows you to search a large sequence dataset against a panel of differentdatabases to build up a picture of where the sequences in your data originate. It was built as a QC check forsequencing pipelines but may also have uses in metagenomicsstudies where mixed samples are expected. Although the program wasn t built with any particulartechnology in mind it is probably only really suitable forprocessing short reads due to the use of bowtie/bowtie2 as the searching application.The program generates both text and graphical output totell you what proportion of your library was able to map, either uniquely or in more than one location, against eachof the databases in your search set.
Download : http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/fastq_screen_v0.4.4.tar.gz
Usage : #fastq_screen [OPTION]... [FastQ FILE]...
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])