Ray 2.3.1 – Parallel Genome Assemblies for Parallel DNA sequencing

Ray 2.3.1

:: DESCRIPTION

Ray is a parallel software that computes de novo genome assemblies with next-generation sequencing data.

::DEVELOPER

Sébastien Boisvert

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Mac OsX/Windows
  • C++ Compiler

:: DOWNLOAD

 Ray

:: MORE INFORMATION

Citation

Genome Biol. 2012 Dec 22;13(12):R122. doi: 10.1186/gb-2012-13-12-r122.
Ray Meta: scalable de novo metagenome assembly and profiling.
Boisvert S, Raymond F, Godzaridis E, Laviolette F, Corbeil J.

Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies.
Boisvert S, Laviolette F, Corbeil J.
Journal of Computational Biology November 2010, 17(11): 1519-1533.

Spherical – An iterative approach for Large Metagenome Assemblies

Spherical

:: DESCRIPTION

Spherical is an iterative approach to assembling metagenomic datasets. Spherical has been designed to produce a more complete assembly from deep sequenced metagenomic data.

::DEVELOPER

The Creevey Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

Spherical

:: MORE INFORMATION

Citation

Hitch, Thomas CA, and Christopher J. Creevey.
Spherical: an iterative workflow for assembling metagenomic datasets.
BMC bioinformatics 19.1 (2018): 20.”

SWALO – Scaffolding with Assembly Likelihood Optimization

SWALO

:: DESCRIPTION

SWALO is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing.

::DEVELOPER

Pachter Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  •  Bowtie 2

:: DOWNLOAD

SWALO

:: MORE INFORMATION

 

DiscoverY – Y-contig Identification from Whole Genome Assemblies

DiscoverY

:: DESCRIPTION

DiscoverY is a tool to shortlist Y-specific contigs from an assembly of male whole genome sequencing data, based on exact k-mer matches with a female.

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

DiscoverY

:: MORE INFORMATION

Citation:

Rangavittal, S., Stopa, N., Tomaszkiewicz, M. et al.
DiscoverY: A Classifier for Identifying Y Chromosome Sequences in Male Assemblies
BMC Genomics (2019) 20: 641.

treecat – Phylogenetic Comparative Assembly

treecat

:: DESCRIPTION

treecat (phylogenetic tree based contig arrangement tool) takes several genomes and their relationships in a phylogenetic tree into account to estimate a possible ordering of the contigs.

::DEVELOPER

treecat team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac / Windows
  • Java

:: DOWNLOAD

treecat

:: MORE INFORMATION

Citation

Husemann, P. & Stoye, J.
Phylogenetic comparative assembly
Algorithms for Molecular Biology, 2010, Vol. 5(1), pp. 3

r2cat – Synteny Plots & Comparative Assembly

r2cat

:: DESCRIPTION

r2cat (related reference based contig arrangement tool) can be used to order a set of contigs with respect to a single reference genome. This is done by mapping the contigs onto the reference using a q-gram filter. The mapping is visualized in a synteny plot.

::DEVELOPER

r2cat team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac / Windows
  • Java

:: DOWNLOAD

r2cat

:: MORE INFORMATION

Citation

Husemann, P. & Stoye, J.
r2cat: synteny plots and comparative assembly
Bioinformatics, 2010, Vol. 26(4), pp. 570-571

ShoRAH v1.9.95 – Short Reads Assembly into Haplotypes

ShoRAH v1.9.95

:: DESCRIPTION

ShoRAH is a software package that allows for inference about the structure of a population from a set of short sequence reads as obtained from ultra-deep sequencing of a mixed sample. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.

::DEVELOPER

the Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ShoRAH

:: MORE INFORMATION

Citation

Zagordi O, Bhattacharya A, Eriksson N, Beerenwinkel N (2011)
ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data.
BMC Bioinformatics, vol. 12 p. 119

HaploClique 1.3.1 – Viral Quasispecies Assembly from Paired-end data

HaploClique 1.3.1

:: DESCRIPTION

HaploClique is a computational approach to reconstruct the structure of a viral quasispecies from next-generation sequencing data as obtained from bulk sequencing of mixed virus samples.

::DEVELOPER

the Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 HaploClique

:: MORE INFORMATION

Citation:

Viral quasispecies assembly via maximal clique enumeration.
Töpfer A, Marschall T, Bull RA, Luciani F, Schönhuth A, Beerenwinkel N.
PLoS Comput Biol. 2014 Mar 27;10(3):e1003515. doi: 10.1371/journal.pcbi.1003515.

HapTree 1.0 – Polyploid Haplotype Assembly tool

HapTree 1.0

:: DESCRIPTION

HapTree is a polyploid haplotype assembly tool based on a statistical framework.

::DEVELOPER

Berger Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Python

:: DOWNLOAD

  HapTree

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2014 Mar 27;10(3):e1003502. doi: 10.1371/journal.pcbi.1003502. eCollection 2014.
HapTree: a novel Bayesian framework for single individual polyplotyping using NGS data.
Berger E, Yorukoglu D, Peng J, Berger B

MetaCompass v2.0-beta – Reference-guided Assembly of Metagenomes

MetaCompass v2.0-beta

:: DESCRIPTION

MetaCompass represents the first effective approach for reference-guided metagenomic assembly of low-abundance bacterial genomes that can complement and improve upon de novo metagenomic assembly methods.

::DEVELOPER

Treangen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

MetaCompass

:: MORE INFORMATION