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Query : Assembler [subsection]

Online Tools (10)

ABySS

Assembler

 

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. We propose MPI version using 4 cores on the platform.

Author(s)

Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ


Version

1.2.1


Subsections

Assembler


Tags

parallel - De novo


Edena

Assembler

 

Edena (Exact DE Novo Assembler) is an assembler dedicated to process the millions of very short reads produced by the Illumina Genome Analyzer. Edena is based on the traditional overlap layout paradigm. All exact overlaps between any pair of reads are computed and structured in a graph (overlap step). Basically, the reads are indexed in a prefix array and overlaps are revealed by dichotomic search in the arrays. The graph is then analyzed to remove transitive and spurious edges (layout step). Finally, contigs that can be assembled following unambiguous path in the graph are given as output. Edena allows to produce contigs of several kbp with a near full coverage of the bacterial genome being sequenced.

Author(s)

D. Hernandez, P. François, L. Farinelli, M. Osteras, and J. Schrenzel


Version

2.1.1


Subsections

Assembler


Tags

De novo


Euler

Assembler

 

EULER-SR is a program for de novo assembly of reads. Contrary to the overlap-layout approach, EULER-SR uses a de Bruijn graph to construct an assembly. The assembly of a genome corresponds to an Eulerian path in the de Bruijn graph. Long (possibly erroneous) reads, and mate-pairs are used to determine parts of the correct Eulerian traversal in the assembly.

Author(s)

Mark Chaisson, Pavel Pevzner, Dumitru Brinza, Haixu Tang, Glenn Tesler


Version

1.1.2


Subsections

Assembler


Tags

De novo


Velvet

Assembler

 

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. Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.

Author(s)

Daniel Zerbino and Ewan Birney


Version

0.7


Subsections

Assembler


Tags

De novo


BWA Sampe

Mapping

 

Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates. Please see the BWA manual page for more information.

Author(s)

Heng Li, Chi-Kwong Wong


Version

0.5.8


Subsections

Mapping - Assembler


Tags

bwa


CAP3

Assembler

 

The program has a capability to clip 5′ and 3′ low-quality regions of reads. It uses base quality values in computation of overlaps between reads, construction of multiple sequence alignments of reads, and generation of consensus sequences. The program also uses forward–reverse constraints to correct assembly errors and link contigs.

Author(s)

Huang, X. and Madan, A.


Version

1


Subsections

Assembler


Tags

under development


BWA Samse

Assembler

 

Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates. Please see the BWA manual page for more information.

Author(s)

Heng Li, Chi-Kwong Wong


Version

0.5.8


Subsections

Assembler - Mapping


Tags

bwa


After read cleaning this pipeline will call Abyss for denovo assembly in contigs. The resulting contigs can be further assembled with CAP3. The contigs are then blasted against a provided multi-fasta file and/or ncbi databases. If a blastx on nr is chosen the result can be used to annotate the best hits with blast2go.

Author(s)

MBB dev


Version

1


Subsections

Pipeline - Blast - Assembler


Tags

De novo


AAA sssss aaa

Author(s)

Khalid


Version

1


Subsections

Pipeline - Assembler


Tags

De novo


Softwares (3)

PopPhyl

Tool

  

The PopPhyl project provides a set of publicly available tools C++ code to achieve SNP and genotype calling (with home made algorithms). Also are provided wrappers to use this tools in the Galaxy platforms.

Executables tools

  • Reads2SNP C++ executable (Static compilation for 32, 64 bits Linux and binary for MacOS)(download)
  • dNdSpiNpiS C++ executable (Static compilation for 64 bits Linux)(download)
  • ORF extractor perl script (download)
Galaxy-related tools

Author(s)

Nicolas Galtier et al.


Version

1


Platform

Linux - Windows - Mac


Source

Yes


Downloads

0


Subsections

Tool - Mapping - Assembler


Tags

ISEM




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