Référentiel des outils installés sur la plateforme Migale
La liste des packages R installés sur la plateforme Migale est disponible ici.
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-pair (version 1.0 - 2019-09-17)
Rewrite paired end fastq files to make sure that all reads have a mate and to separate out singletons. This code does one thing: it takes two fastq files, and generates four fastq files. That's right, for free it doubles the number of fastq files that you have!! Usually when you get paired end read files you have two files with a /1 sequence in one and a /2 sequence in the other (or a /f and /r or just two reads with the same ID). However, often when working with files from a third party source (e.g. the SRA) there are different numbers of reads in each file (because some reads fail QC). Spades, bowtie2 and other tools break because they demand paired end files have the same number of reads.
Download : https://github.com/linsalrob/fastq-pair
Documentation : https://github.com/linsalrob/fastq-pair
Usage : # fastq_pair [options] [fastq file 1] [fastq file 2]
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]...
fastSpar (version 0.0.10 - 2019-08-31)
SparCC determines correlations between OTUs
Download : https://github.com/scwatts/fastspar
Remarque : If you use this tool, please cite the FastSpar paper and original SparCC paper: Watts, S. C., Ritchie, S. C., Inouye, M., & Holt, K. E. (2018). FastSpar: rapid and scalable correlation estimation for compositional data. Bioinformatics. doi: 10.1093/bioinformatics/bty734 Friedman, J. & Alm, E.J. (2017). Inferring correlation networks from genomic survey data. PLoS Comput. Biol. 8, e1002687.
Usage : #fastspar [options] --otu_table
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])
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.
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]