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.

Assemblage de séquences nucléiques


VersionMAJ

ALLPATHS-LG

2012-03-13DownloadDoc
ALLPATHS-LG is a de Bruijn graph-based de novo assembler for large (and small) genomes. ALLPATHS-LG is being developed by scientists at the Broad Institute.

Remarque
Run Unix # Run Web #

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amos

3.1.02013-08-12DownloadDoc
AMOS: A Modular Open-Source Assembler

Remarque
Run Unix # Run Web #

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arachne

3.12008-07-29DownloadDoc
Arachne is a tool for assembling genome sequences from whole genome shotgun reads, mostly in forward-reverse pairs obtained by sequencing clone ends.

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Run Unix # Run Web #

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BCM trace viewer

1.5DownloadDoc
A Java application/applet to display .scf traces and phred quality values.

Remarque
Run Unix # bcm-trace-view -s { -q }Run Web #

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cap3

3.02014-05-06DownloadDoc
Similar to phrap, CAP3 takes individual sequences and assembles them into sequence.s

Remarque
Run Unix # cap3Run Web #

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Celera Assembler (wgs)

5.42009-10-29DownloadDoc
Celera Assembler is scientific software for DNA research. It can reconstruct long sequences of genomic DNA from the fragmentary data produced by whole-genome shotgun sequencing. The Celera Assembler is mature, efficient, open-source software written mostly in C for unix operating systems.

Remarque This whole-genome shotgun (WGS) assembler software suite, also known as Celera Assembler, implements sophisticated algorithms for the reconstruction of genomic DNA sequence from data produced by a WGS sequencing experiment.
Run Unix # Run Web #

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consed

22.02014-04-30DownloadDoc
Consed/Autofinish is a tool for viewing, editing, and finishing sequence assemblies created with phrap. Finishing capabilities include allowing the user to pick primers and templates, suggesting additional sequencing reactions to perform, and facilitating checking the accuracy of the assembly using digest and forward/reverse pair information.

Remarque Voir aussi autofinishs (http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11282977s)
Run Unix # consedRun Web #

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FinchTV

1.3.12008-10-14DownloadDoc
FinchTV (Finch Trace Viewer), a cross-platform graphical viewer for chromatogram files.s

Remarque
Run Unix # finchtvRun Web #

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GapCloser

1.122015-07-13DownloadDoc
GapCloser for SOAPdenovo The GapCloser is designed to close the gaps emerging during the scaffolding process by SOAPdenovo or other assembler, using the abundant pair relationships of short reads. GapCloser aims for large plant and animal genomes, although it also works well on bacteria and fungi genomes.

Remarque
Run Unix # GapCloser [options]Run Web #

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ICORN

0.972010-11-03DownloadDoc
iCORN (iterative correction of reference nucleotides) can correct genome sequences with short reads. Reads are mapped iteratively against the genome sequences, so far by SSAHA. Discrepancies between the multiple alignments of the mapping reads and reference are corrected, if by the correction the amount of perfect mapping reads doesn't decrease.

Remarque
Run Unix # cf. http://icorn.sourceforge.net/example.htmlRun Web #

VersionMAJ

khmer

2.02015-11-25DownloadDoc
The khmer software is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.

Remarque
Run Unix # -Run Web #

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Megahit

1.0.4-beta2016-03-17DownloadDoc
MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Remarque
Run Unix # megahit [options] {-1 -2 | --12 | -r } [-o ]Run Web #

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mira

4.02014-11-18DownloadDoc
MIRA is a Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina. It can perform Hybrid de-novo assemblies as well as SNP and mutations discovery for mapping assemblies.

Remarque
Run Unix # miraRun Web #

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mktrace

0.001017 2005-07-30DownloadDoc
This program reads a FASTA file and creates a chromatogram stored in an SCF file and a corresponding phd file. The SCF file contains minimal information at this time. If a quality value FASTA file exists, mktrace uses those quality values in the phd file, otherwise it sets the quality values to the pre-determined values. mktrace produces a fake trace that could be used by Phred/Phrap packages.

Remarque Fait parti du package consed
Run Unix # mktrace G0771A003_114.s1.seq G0771A003_114.s1.scfRun Web #

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MOSAIK assembler

1.1.00212011-06-06DownloadDoc
MOSAIK is a reference-guided assembler comprising of four main modular programs: * MosaikBuild * MosaikAligner * MosaikSort * MosaikAssembler. MosaikBuild converts various sequence formats into Mosaik’s native read format. MosaikAligner pairwise aligns each read to a specified series of reference sequences. MosaikSort resolves paired-end reads and sorts the alignments by the reference sequence coordinates. Finally, MosaikAssembler parses the sorted alignment archive and produces a multiple sequence alignment which is then saved into an assembly file format.

Remarque
Run Unix # MosaikAligner MosaikAssembler MosaikBuild MosaikCoverage MosaikDupSnoop MosaikJump MosaikMerge MosaikSort MosaikTextRun Web #

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newbler

2.62011-07-06DownloadDoc
Newbler is a package of three data analysis applications made by Roche 454 : the GS De Novo Assembler (with or without contig scaffolding using Paired End reads), the GS Reference Mapper, and the GS Amplicon Variant Analyzer (AVA). An additional application, the GS Run Browser, is an interactive Run browser/ troubleshooting tool which displays graphically the images, some intermediate data, and various output metrics from a sequencing Run. The software package also includes the SFF Tools commands for handling and using the data files (called Standard Flowgram Format or SFF files) that hold the sequencing trace data.

Remarque
Run Unix # newblerRun Web #

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opera

2.02015-03-02DownloadDoc
Opera (Optimal Paired-End Read Assembler) is a sequence assembly program.

Remarque To cite Opera please use the following citation: Song Gao, Wing-Kin Sung, Niranjan Nagarajan. Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. Journal of Computational Biology, Sept. 2011, doi:10.1089/cmb.2011.0170.
Run Unix # opera OR opera Run Web #

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phrap

1.0905182010-01-18DownloadDoc
phrap is a program for assembling shotgun DNA sequence data. Among other features, it allows use of the entire read and not just the trimmed high quality part, it uses a combination of user-supplied and internally computed data quality information to improve assembly accuracy in the presence of repeats, it constructs the contig sequence as a mosaic of the highest quality read segments rather than a consensus, it provides extensive assembly information to assist in trouble-shooting assembly problems, and it handles large datasets.

Remarque Marche avec cross_match et swat, loco et cluster La version manyreads permet de lire plus de trace.
Run Unix # phrapRun Web #

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phrapview

DownloadDoc
visualisateur des resultats d'assemblage issus de phraps

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Run Unix # Run Web #

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phred

020425.c2005-07-27DownloadDoc
Phred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files. Phred can read trace data from chromatogram files in the SCF, ABI, and ESD formats. It automatically determines the file format, and whether the chromatogram file was compressed using gzip, bzip2, or UNIX compress. After calling bases, phred writes the sequences to files in either FASTA format, the format suitable for XBAP, PHD format, or the SCF format. Quality values for the bases are written to FASTA format files or PHD files, which can be used by the phrap sequence assembly program in order to increase the accuracy of the assembled sequence. phred, phrap, consed are Unix programs that work as a group for analysis of new DNA sequences. They do the following: phred: Base calling and quality assignments phrap: Contig formation and new quality assignments consed: Visual X-Windows graphic interface, to view and edit alignments and contigs, and to view the original traces

Remarque
Run Unix # phred ou phredPhrapRun Web #

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phredPhrap

030415DownloadDoc
It runs phred on all *new* reads (reads for which there is no phd file. It runs determineReadTypes.perl so consed, autofinish, and phrap will understand your read naming convention Then it runs crossmatch to screen them for vector. Then it runs phd2fasta to create 2 fasta files (one containing read bases and one containing read quality. These are of the highest versions of each read (in case any editing has been done). It runs phrap It runs transferConsensusTags to transfer any consensus tags from the newest old ace file to the one phrap created in step 4 It runs tagRepeats.perl to tag any common repeats (such as ALU) that you want to have automatically tagged for the benefit of consed users. See README.txt "INSTALLING CONSED Typically, you just type: phredPhrap Within the project, there are 3 directories: chromat_dir (with the chromats), phd_dir (with the phd files) and edit_dir (with the ace files and other files). You type "phredPhrap" from within edit_dir.

Remarque Frontal pour la suite phred phrap
Run Unix # phrepPhrapRun Web #

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phusion

2.1c2008-07-29DownloadDoc
Phusion Assembler --- Phusion is a software package for assembling genome sequences from whole genome shotgun(WGS) reads. The Phusion assembler takes WGS reads, mostly paired with known insert sizes, as input along with quality score assigned for each base and produces a set of supercontigs (scaffords) .

Remarque
Run Unix # Run Web #

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platanus

1.2.12015-03-06DownloadDoc
Platanus is a de novo assembler designed to assemble high-throughput data. It can handle highly heterozygotic samples. The following is the assembly outline. First, it constructs contigs using the algorithm based on de Bruijn graph. Second, the order of contigs is determined according to paired-end (mate-pair) data and constructs scaffolds. Finally, paired-end reads localized on gaps in scaffolds are assembled and gaps are closed.

Remarque To reference the Platanus assembler, please cite : Kajitani R. et al. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Research 24:1384-95.
Run Unix # Usage: platanus Command [options] Command: assemble, scaffold, gap_close Run Web #

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SOAPdenovo

1.042010-08-23DownloadDoc
SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way.

Remarque
Run Unix # soapdenovo [option]Run Web #

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staden

2.0.0b72011-02-03DownloadDoc
The Staden Package is a set of tools covering sequence assembly, editing and analysis. Gap4 performs sequence assembly, contig ordering based on read pair data, contig joining based on sequence comparisons, assembly checking, repeat searching, experiment suggestion, read pair analysis and contig editing. Pregap4 provides a graphical user interface to set up the processing required to prepare trace data for assembly or analysis. Trev is a rapid and flexible viewer and editor for ABI, ALF, SCF and ZTR trace files. Prefinish analyses partially completed sequence assemblies and suggests the most efficient set of experiments to help finish the project. Tracediff and hetscan automatically locate mutations by comparing trace data against reference traces. Spin analyses nucleotide sequences to find genes, restriction sites, motifs, etc. It can perform translations, find open reading frames, count codons, etc.

Remarque
Run Unix # http://staden.sourceforge.net/overview.htmlRun Web #

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TGI

2005-07-25DownloadDoc
TGI Clustering tools (TGICL): a software system for fast clustering of large EST datasets This package automates clustering and assembly of a large EST/mRNA dataset. The clustering is performed by a slightly modified version of NCBI's megablast , and the resulting clusters are then assembled using CAP3 assembly program. TGICL starts with a large multi-FASTA file (and an optional peer quality values file) and outputs the assembly files as produced by CAP3.

Remarque
Run Unix # tgicl , cap3...Run Web #

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vcake

1.02008-07-30DownloadDoc
VCAKE is a genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error. This software is currently geared towards de novo assembly of Illumina's Solexa Sequencing data.

Remarque
Run Unix # perl -S vcake.plRun Web #

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velvet

1.2.072013-08-07DownloadDoc
Sequence assembler for very short reads. Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.

Remarque
Run Unix # velveth # velvetgRun Web #

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Xgenovo

-2016-03-17DownloadDoc
Metagenomes present assembly challenges, when assembling multiple genomes from mixed reads of multiple species. An assembler for single genomes can’t adapt well when applied in this case. A metagenomic assembler, Genovo, is a de novo assembler for metagenomes under a generative probabilistic model. Genovo assembles all reads without discarding any reads in a preprocessing step, and is therefore able to extract more information from metagenomic data and, in principle, generate better assembly results. Paired end sequencing is currently widely-used yet Genovo was designed for 454 single end reads. In this research, we attempted to extend Genovo by incorporating paired-end information, named Xgenovo, so that it generates higher quality assemblies with paired end reads.

Remarque
Run Unix # assemble - finalize Run Web #

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