Faucet v0.5 – Streaming de novo Assembly Graph Construction

Faucet v0.5

:: DESCRIPTION

Faucet is an streaming metagenome assembler. It uses low memory and disk space and achieves highly contiguous assemblies.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Faucet

:: MORE INFORMATION

Citation

Bioinformatics. 2018 Jan 1;34(1):147-154. doi: 10.1093/bioinformatics/btx471.
Faucet: streaming de novo assembly graph construction.
Rozov R, Goldshlager G, Halperin E, Shamir R.

TRUST4 v0.1.1 – TCR and BCR Assembly from RNA-seq data

TRUST4 v0.1.1

:: DESCRIPTION

TRUST (T cell receptor Repertoire Utilities for Solid Tissue/Tumor) is a toolbox for analyzing T cell receptors in solid tumors using unselected RNA-seq data based on de novo assembly.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

TRUST

:: MORE INFORMATION

 

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.

MaLTA – Transcriptome Assembly and Quantification from Ion Torrent RNA-Seq data

MaLTA

:: DESCRIPTION

MaLTA is a method for simultaneous transcriptome assembly and quantification from Ion Torrent RNA-Seq data.

::DEVELOPER

Georgia State University NGS Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 MaLTA

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Jul 14;15 Suppl 5:S7. doi: 10.1186/1471-2164-15-S5-S7. Epub 2014 Jul 14.
Transcriptome assembly and quantification from Ion Torrent RNA-Seq data.
Mangul S, Caciula A, Al Seesi S, Brinza D, M?ndoiu I, Zelikovsky A.

bcm-ace-plots – Reads in an Ace format Assembly File produced by the Phrap

bcm-ace-plots

:: DESCRIPTION

bcm-ace-plots reads in an Ace format assembly file produced by the Phrap (Green et al.) assembly software. Using special tags in the read names, bcm-ace-plots will plot the template coverage, the template span, the coverage, the BAC coverage, the WGS coverage, quality, and high quality discrepancies.

::DEVELOPER

Human Genome Sequencing Center, Baylor College of Medicine

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  MacOsX
  • Java

:: DOWNLOAD

bcm-ace-plots

:: MORE INFORMATION

ATLAS GapFill 2.2 – Deals with the Repetitive Gap Assembly problem

ATLAS GapFill 2.2

:: DESCRIPTION

ATLAS GapFill deals with the repetitive gap assembly problem by using the unique gap-flanking sequences to group reads and convert the problem to a local assembly task. Localizing the assembly reduces the numbers of repeats in the assembly, allows more data to be incorporated, and allows for gaps to be filled.

::DEVELOPER

Human Genome Sequencing Center, Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ATLAS GapFill

:: MORE INFORMATION

GAM-NGS 1.1b – Genome Assemblies Merger for Next Generation Sequencing

GAM-NGS 1.1b

:: DESCRIPTION

GAM-NGS is able to merge two or more assemblies and it rteturns an improved assembly (more contiguous and more correct). GAM-NGS shows its full potential with multi-library Illumina-based projects.

::DEVELOPER

GAM-NGS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GAM-NGS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013;14 Suppl 7:S6. doi: 10.1186/1471-2105-14-S7-S6. Epub 2013 Apr 22.
GAM-NGS: genomic assemblies merger for next generation sequencing.
Vicedomini R, Vezzi F, Scalabrin S, Arvestad L, Policriti A.

Cortex 1.05.21 – Genome Assembly and Variation Analysis

Cortex 1.05.21

:: DESCRIPTION

Cortex is an efficient and low-memory software framework for analysis of genomes using sequence data. There are two main executables, being developed in parallel streams: cortex_con (primary contact Mario Caccamo) is for consensus genome assembly, and cortex_var (primary contact Zamin Iqbal) is for variation and population assembly.

::DEVELOPER

Cortex team

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux
  • C compiler

:: DOWNLOAD

 Cortex

:: MORE INFORMATION

Citation

Nat Genet. 2012 Jan 8;44(2):226-32. doi: 10.1038/ng.1028.
De novo assembly and genotyping of variants using colored de Bruijn graphs.
Iqbal Z, Caccamo M, Turner I, Flicek P, McVean G.

RAMPART 0.12.2 – A Workflow Management System for de novo Genome Assembly

RAMPART 0.12.2

:: DESCRIPTION

RAMPART is a de novo assembly pipeline that makes use of third party-tools and High Performance Computing resources. It can be used as a single interface to several popular assemblers, and can perform automated comparison and analysis of any generated assemblies.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /Linux/ MacOsX
  • JRE

:: DOWNLOAD

 RAMPART

:: MORE INFORMATION

Citation

RAMPART: a workflow management system for de novo genome assembly.
Mapleson D, Drou N, Swarbreck D.
Bioinformatics. 2015 Jan 30. pii: btv056.

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