Tag: Assembly

PyroCleaner 1.3 – Clean 454 Pyrosequencing Reads in order to ease the Assembly Process

PyroCleaner 1.3

:: DESCRIPTION

The pyrocleaner is intended to clean the reads included in the sff file in order to ease the assembly process. It enables filtering sequences on different criteria such as length, complexity, number of undetermined bases which has been proven to correlate with poor quality and multiple copy reads. It also enables to clean paired-ends sff files and generates on one side a sff with the validated paired-ends and on the other the sequences which can be used as shotgun reads.

::DEVELOPER

the bioinformatic plateforms of Genotoul.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  PyroCleaner

:: MORE INFORMATION

Citation

Mariette J, Noirot C, Klopp C.
Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool.
BMC Research Notes 2011, 4:149

Reconciliator 2.0 – The tool for Merging Assemblies

Reconciliator 2.0

:: DESCRIPTION

Reconciliator is the tool for merging assemblies.

::DEVELOPER

IPST GENOME ASSEMBLY GROUP

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Reconciliator

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Jan 1;24(1):42-5. Epub 2007 Dec 5.
Assembly reconciliation.
Zimin AV, Smith DR, Sutton G, Yorke JA.

GenSeed 1.0.22 – Seed-driven progressive Assembly program

GenSeed 1.0.22

:: DESCRIPTION

GenSeed is a Perl program that implements a seed-driven recursive assembly consisting of cycles comprising a similarity search, read selection and assembly. The iterative process results in a progressive extension of the original seed sequence.

::DEVELOPER

GenSeed Team 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GenSeed

:: MORE INFORMATION

Citation:

Sobreira, T.J.P. & Gruber, A. (2008).
Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data.
Bioinformatics, doi: 10.1093/bioinformatics/btn283

GS De Novo Assembler – de novo DNA Sequence Assembly

GS De Novo Assembler

:: DESCRIPTION

GS De Novo Assembler (Newbler) is a software package for de novo DNA sequence assembly. It is designed specifically for assembling sequence data generated by the 454 GS-series of pyrosequencing platforms sold by 454 Life Science, a Roche diagnostic.

::DEVELOPER

454 Sequencing 

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GS De Novo Assembler

:: MORE INFORMATION

Cleaner 1.03 – Assembly of Informative, Transcript-specific Probe-clusters

Cleaner 1.03

:: DESCRIPTION

Cleaner: R-system software package for the assembly of informative, transcript-specific probe-clusters for Affymetrix expression microarrays.

::DEVELOPER

the Califano lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Cleaner

:: MORE INFORMATION

PGAAS 1.0 – Prokaryotic Genome Assembly Assistant System

PGAAS 1.0

:: DESCRIPTION

PGAAS is prokaryotic genome assembly assistant system. The approach upon which PGAAS is based is to confirm the order of contigs and fill gaps between contigs through peptide links obtained by searching each contig end with BLASTX against protein database.

::DEVELOPER

Center for Bioinformatics, PKU.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MySQL
  • PHP
  • Apache

:: DOWNLOAD

 PGAAS

:: MORE INFORMATION

Citation:

PGAAS: a prokaryotic genome assembly assistant system.
Yu Z, Li T, Zhao J, Luo J.
Bioinformatics. 2002 May;18(5):661-5.

DNPTrapper 1.0 – Assembly Editing & Visualization Tool

DNPTrapper 1.0

:: DESCRIPTION

DNPTrapper, a shotgun sequence finishing tool, designed to address the key sequence assembly problems caused by repeated regions in a genome. The program detects and visualizes single nucleotide differences between nearly identical repeat copies, and offers the overview and flexibility needed to rapidly resolve complex regions within a working session. The use of a database allows large amounts of data to be stored and handled, and allows viewing of mammalian size genomes. With DNPTrapper, it is possible to separate repeated regions that previously were considered impossible to resolve, and finishing tasks that previously took days or weeks can be resolved within hours or even minutes.

::DEVELOPER

Tammi Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

DNPTrapper

:: MORE INFORMATION

Citation:

BMC Bioinformatics, 2006 Mar 20; 7:155
DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions.
Arner, E, Tammi, MT, Tran, AN, Kindlund, E, Andersson B.

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