Tag: Assembling

SSAKE 4.0 – Assembling Millions of short DNA Sequences

SSAKE 4.0

:: DESCRIPTION

SSAKE is a genomics application for assembling millions of very short DNA sequences.SSAKE is designed to help leverage the information from short sequence reads by stringently assembling them into contiguous sequences that can be used to characterize novel sequencing targets.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Perl

:: DOWNLOAD

 SSAKE

:: MORE INFORMATION

Citation

René L Warren, Granger G Sutton, Steven JM Jones, Robert A Holt. 2007
Assembling millions of short DNA sequences using SSAKE.
bioinformatics. 23:500-501.

Rainbow v2.0.4 – Clustering and Assembling Short Reads, especially for RAD

Rainbow v2.0.4

:: DESCRIPTION

Rainbow package consists of several programs used for RAD-seq related clustering and de novo assembly.

::DEVELOPER

Rainbow team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 Rainbow

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 1;28(21):2732-7. doi: 10.1093/bioinformatics/bts482.
Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads.
Chong Z, Ruan J, Wu CI.

PlasmidTron 0.4.1 – Assembling the cause of Phenotypes and Genotypes from NGS data

PlasmidTron 0.4.1

:: DESCRIPTION

PlasmidTron utilizes the phenotypic data normally available in bacterial population studies, such as antibiograms, virulence factors, or geographical information, to identify traits that are likely to be present on DNA that can randomly reassort across defined bacterial populations. It is also possible to use this methodology to associate unknown genes/sequences (e.g. plasmid backbones) with a specific molecular signature or marker (e.g. resistance gene presence or absence) using PlasmidTron. PlasmidTron uses a k-mer-based approach to identify reads associated with a phylogenetically unlinked phenotype.

::DEVELOPER

Pathogen Informatics, Wellcome Trust Sanger Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

PlasmidTron

:: MORE INFORMATION

Citation

PlasmidTron: assembling the cause of phenotypes and genotypes from NGS data,
Andrew J Page, Alexander Wailan, Yan Shao, Kim Judge, Gordon Dougan, Elizabeth J. Klemm, Nicholas R. Thomson, Jacqueline A. Keane, 2018,
Microbial Genomics 4(3); doi: 10.1099/mgen.0.000164

Curtain 0.2.3 beta – Assembling large Genomes from Short Read Sequences

Curtain 0.2.3 beta

:: DESCRIPTION

Curtain is an assembler of next generation sequence. Curtain is a Java wrapper around next-generation assemblers such as Velvet, which allows the incremental introduction of read-pair information into the assembly process.

::DEVELOPER

Matthias Haimel, email: mhaimel.ebi@googlemail.com

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

  Curtain

:: MORE INFORMATION