Arachne 4.6233 – Whole-genome Shotgun Assembler

Arachne 4.6233

:: DESCRIPTION

ARACHNE is a program for assembling data from whole genome shotgun sequencing experiments. It was designed for long reads from Sanger sequencing technology, and has been used extensively to assemble many genomes, including many that are large and highly repetitive.

::DEVELOPER

Bonnie Berger 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Arachne

:: MORE INFORMATION

Citation

Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. 2002.
ARACHNE: a whole-genome shotgun assembler.
Genome Research12: 177–189.

Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP, Zody MC, Lander ES. 2003.
Whole-genome sequence assembly for mammalian genomes: Arachne 2.
Genome Research 13: 91–96.

Gnerre S, Lander ES, Lindblad-Toh K, Jaffe DB. 2009.
Assisted assembly: how to improve a de novo genome assembly by using related species.
Genome Biology10: R88.

ViSpA 02 – Viral Spectrum Assembler

ViSpA 02

:: DESCRIPTION

ViSpA (Viral Spectrum Assembling) implements a novel viral assembling and frequency estimation methods. This software uses a simple error correction, viral variants assembling based on maximum-bandwidth paths in weighted read graphs and frequency estimation via Expectation Maximization on all reads.

::DEVELOPER

Georgia State University NGS Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 ViSpA

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2011;12 Suppl 6:S1. doi: 10.1186/1471-2105-12-S6-S1. Epub 2011 Jul 28.
Inferring viral quasispecies spectra from 454 pyrosequencing reads.
Astrovskaya I, Tork B, Mangul S, Westbrooks K, Măndoiu I, Balfe P, Zelikovsky A.

EagleView 2.2 – Genome Assembler Viewer

EagleView 2.2

:: DESCRIPTION

EagleView is an information-rich genome assembler viewer with data integration capability. EagleView can display a dozen different types of information including base qualities, machine specific trace signals, and genome feature annotations. It provides an easy way for inspecting visually the quality of a genome assembly and validating polymorphism candidate sites (e.g., SNPs) reported by polymorphism discovery tools. It can also facilitate data interpretation and hypothesis generation.

::DEVELOPER

EagleView team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/windows/MacOsX

:: DOWNLOAD

 EagleView

:: MORE INFORMATION

Citation

Weichun Huang and Gabor Marth
EagleView: a genome assembly viewer for next-generation sequencing technologies,
Genome Res.,June 11, 2008

Scallop v0.10.4 – Reference-based Transcriptome Assembler for RNA-seq

Scallop v0.10.4

:: DESCRIPTION

Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts. Scallop achieves this improvement through a novel algorithm that can be proved preserving all phasing paths from reads and paired-end reads, while also achieves both transcripts parsimony and coverage deviation minimization.

::DEVELOPER

Kingsford Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs
  • Boost

:: DOWNLOAD

Scallop

:: MORE INFORMATION

Citation

Nat Biotechnol. 2017 Dec;35(12):1167-1169. doi: 10.1038/nbt.4020.
Accurate assembly of transcripts through phase-preserving graph decomposition.
Shao M, Kingsford C.

KisSplice 2.4.0-p1 – Local Transcriptome Assembler for SNPs and AS events

KisSplice 2.4.0-p1

:: DESCRIPTION

KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler, which enables to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number of biological conditions, and will quantify each variant in each condition. It has been tested on Illumina datasets of up to 300M reads.

::DEVELOPER

KisSplice Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac OS X /  Linux

:: DOWNLOAD

 KisSplice

:: MORE INFORMATION

Citation

Gustavo AT Sacomoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, Marie-France Sagot, Pierre Peterlongo and Vincent Lacroix,
KISSPLICE: de-novo calling alternative splicing events from RNA-seq data.
BMC Bioinformatics 2012, 13(Suppl 6):S5

PEAR 0.9.8 – Pair-End reads AssembleR

PEAR 0.9.8

:: DESCRIPTION

PEAR is an ultrafast, memory-efficient and highly accurate pair-end reads assembler. It is fully parallelized and can run with as low as just a few kilobytes of memory.

::DEVELOPER

The Exelixis Lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PEAR

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 1;30(5):614-20. doi: 10.1093/bioinformatics/btt5
PEAR: A fast and accurate Illumina Paired-End reAd mergeR.
Zhang J, Kobert K, Flouri T, Stamatakis A.

kronos 2.3.0 – Workflow Assembler for Cancer Genome Analytics and Informatics

kronos 2.3.0

:: DESCRIPTION

Kronos is a software platform for facilitating the development and execution of modular, auditable, and distributable bioinformatics workflows.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Python

:: DOWNLOAD

kronos

:: MORE INFORMATION

Citation

Gigascience. 2017 Jul 1;6(7):1-10. doi: 10.1093/gigascience/gix042.
Kronos: a workflow assembler for genome analytics and informatics.
Taghiyar MJ, Rosner J, Grewal D, Grande BM, Aniba R, Grewal J, Boutros PC, Morin RD, Bashashati A, Shah SP

IVA 1.0.9 – Iterative Virus Assembler

IVA 1.0.9

:: DESCRIPTION

IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high and variable depth.

::DEVELOPER

Pathogen Informatics, Wellcome Trust Sanger Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 IVA

:: MORE INFORMATION

Citation

IVA: accurate de novo assembly of RNA virus genomes.
Hunt M, Gall A, Ong SH, Brener J, Ferns B, Goulder P, Nastouli E, Keane JA, Kellam P, Otto TD.
Bioinformatics. 2015 Feb 28. pii: btv120.

EBARDenovo 2.0.1 – Highly-accurate de novo Assembler of Paired-end RNA-Seq

EBARDenovo 2.0.1

:: DESCRIPTION

EBARDenovo is a highly-accurate search-based de novo assembler of paired-end RNA-Seq for advance transcriptomic study.

::DEVELOPER

Frank Hsueh-Ting Chu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX

:: DOWNLOAD

 EBARDenovo

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Apr 15;29(8):1004-1010. Epub 2013 Mar 1.
EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection.
Chu HT, Hsiao WW, Chen JC, Yeh TJ, Tsai MH, Lin H, Liu YW, Lee SA, Chen CC, Tsao TT, Kao CY.