Arrêt de l'ensemble des services de la plateforme Migale à partir du lundi 3 avril 2017

La plateforme Migale sera indisponible du 3 au 10 avril 2017. Cette indisponibilité est dûe à l'arrêt du DataCenter Ile-de-France qui héberge l'infrastructure de la plateforme.

Merci d'avance de votre compréhension.

Pour toutes questions ou informations supplémentaires, merci de contacter help.migale@jouy.inra.fr.

Assignation de lectures courtes


VersionMAJ

abyss

1.5.22014-11-18DownloadDoc
ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.

Remarque
Run Unix # Usage: ABYSS [OPTION]... FILE...Run Web #

VersionMAJ

bfast

0.7.02013-08-12DownloadDoc
BFAST : Blat-like Fast Accurate Search Tool BFAST facilitates the fast and accurate mapping of short reads to reference sequences. Some advantages of BFAST include: * Speed: enables billions of short reads to be mapped quickly. * Accuracy: A priori probabilities for mapping reads with defined set of variants. * An easy way to measurably tune accuracy at the expense of speed.

Remarque
Run Unix # bfast [options]Run Web #

VersionMAJ

bwa

0.7.122015-04-07DownloadDoc
BWA is a fast light-weighted tool that aligns short sequences to a sequence database, such as the human reference genome. By default, BWA finds an alignment within edit distance 2 to the query sequence, except for disallowing gaps close to the end of the query. It can also be tuned to find a fraction of longer gaps at the cost of speed and of more false alignments.

Remarque
Run Unix # bwa [options]Run Web #

VersionMAJ

corona

4.2.22009-09-10DownloadDoc
The SOLiD System Analysis Pipeline Tool (Corona Lite) is an off-instrument SOLiD data analysis software package. It supports functionality for mapping color space reads to large or small genomes, pairing for mate-pair runs, SNP calling and generating consensus sequences.

Remarque
Run Unix # Run Web #

VersionMAJ

GASSST

1.282013-08-25DownloadDoc
GASSST : Global Alignment Short Sequence Search Tool * GASSST finds global alignments of short DNA sequences against large DNA banks. * GASSST strong point is its ability to perform fast gapped alignments. * It works well for both short and longer reads. It currently has been tested for reads up to 500bp. * The software is freely available for download under the CECILL version 2 License.

Remarque http://bioinformatics.oxfordjournals.org/content/26/20/2534.abstract?keytype=ref&ijkey=f5zH80QsuCqixRH
Run Unix # Gassst -d -i -o -p Run Web #

VersionMAJ

maq

0.7.12014-10-02DownloadDoc
Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing machines. It is particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has a preliminary functionality to handle AB SOLiD data.

Remarque
Run Unix # maqRun Web #

VersionMAJ

miRDeep2

2.0.0.72015-02-23DownloadDoc
documentation miRDeep2 documentation What is miRDeep2 miRDeep2 is a software package for identification of novel and known miRNAs in deep sequencing data. Furthermore, it can be used for miRNA expression profiling across samples. Last, a new module for preprocessing of raw Illumina sequencing data produces files for downstream analysis with the miRDeep2 or quantifier module. Colorspace sequencing data is currently not supported by the preprocessing module but it is planed to be implemented. Preprocessing is performed with the mapper.pl script. Quantification and expression profiling is done by the quantifier.pl script. miRNA identification is done by the miRDeep2.pl script.

Remarque
Run Unix # miRDeep2.plRun Web #

VersionMAJ

MPscan

-2013-08-26DownloadDoc
MPscan: fast localisation of multiple reads in genomes

Remarque Please cite THIS paper if you use MPscan. Rivals E., Salmela L., Kiiskinen P., Kalsi P., Tarhio J.Lecture Notes in BioInformatics (LNBI), Springer-Verlag, Vol. 5724, p. 246-260, 2009.
Run Unix # mpscan -hRun Web #

VersionMAJ

novoalign

2.08.012013-08-20DownloadDoc
Novoalign is an aligner for single-ended and paired-end reads from the Illumina Genome Analyser. Novoalign finds global optimum alignments using full Needleman-Wunsch algorithm with affine gap penalties.

Remarque
Run Unix # novoalign [options]Run Web #

VersionMAJ

ProbeMatch

-2010-05-11DownloadDoc
ProbeMatch is a sequence alignment program that finds sequence alignments for short DNA sequences ( 36-50 bp ). Unlike other programs such as eland and soap that perform ungapped alignment allowing up to 2 substitution, Probematch performs *gapped* alignment, allowing up to 3 errors including substitution, insertion, and deletion.

Remarque
Run Unix # probematch [options] ou # probematch --help Run Web #

VersionMAJ

seqmap

1.0.122009-02-19DownloadDoc
SeqMap is a tool for mapping large amount of oligonucleotide to the genome. It is designed for finding all the places in a genome where an oligonucleotide could potentially come from. SeqMap can efficiently map as many as dozens of millions of short sequences to a genome of several billions of nucleotides. While doing the mapping, several mutations as well as insertions/deletions of the nucleotide bases in the sequences can be tolerated and furthermore detected. Various input and output formats are supported, as well as many command line options for tuning almost every steps in the mapping process.

Remarque Publication: http://dx.doi.org/10.1093/bioinformatics/btn429
Run Unix # seqmapRun Web #

VersionMAJ

soap

2.202014-08-23DownloadDoc
SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment. The new program features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer. Compared to soap v1, it is one order of magnitude faster. It require only 2 minutes aligning one million single-end reads onto the human reference genome. Another remarkable improvement of SOAPaligner is that it now supports a wide range of the read length.

Remarque To run SOAPaligner, we need to build index files for the reference genome (2bwt-builder), and then search reads against the formatted index files(soap).
Run Unix # soapRun Web #

VersionMAJ

ssaha2

2.5.22014-08-20DownloadDoc
SSAHA (Sequence Search and Alignment by Hashing Algorithm) is an algorithm for very fast matching and alignment of DNA sequences. It achieves its fast search speed by encoding sequence information in a perfect hash function.

Remarque
Run Unix # ssaha2Run Web #

VersionMAJ

ssake

3.22008-07-30DownloadDoc
SSAKE is a genomics application for assembling millions of very short DNA sequences.sIt is an easy-to-use, robust, reliable and tractable clustering algorithm for very short sequence reads, such as those generated by Illumina Ltd.

Remarque
Run Unix # ssake.plRun Web #

VersionMAJ

tophat

2.0.92013-07-10DownloadDoc
TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

Remarque
Run Unix # tophat -hRun Web #

Menu principal

Page | by Dr. Radut