Artemis v18.0.3 – Genome Browser and Annotation Tool

Artemis v18.0.3

:: DESCRIPTION

Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.

::DEVELOPER

the Sanger Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Java

:: DOWNLOAD

Artemis

:: MORE INFORMATION

Citation

Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA and Barrell B
Artemis: sequence visualization and annotation.
Bioinformatics (Oxford, England) 2000;16;10;944-5

GenVisR 1.16.1 – Genome Data Visualizations

GenVisR 1.16.1

:: DESCRIPTION

Intuitively visualizing and interpreting data from high-throughput genomic technologies continues to be challenging.GenVisR (“Genomic Visualizations in R”) attempts to alleviate this burden by providing highly customizable publication-quality graphics supporting multiple species and focused primarily on a cohort level (i.e., multiple samples/patients). GenVisR attempts to maintain a high degree of flexibility while leveraging the abilities of ggplot2 and bioconductor to achieve this goal.

::DEVELOPER

The Griffith Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • R/ BioConductor

:: DOWNLOAD

 GenVisR

:: MORE INFORMATION

Citation

GenVisR: Genomic Visualizations in R.
Skidmore ZL, Wagner AH, Lesurf R, Campbell KM, Kunisaki J, Griffith OL, Griffith M.
Bioinformatics. 2016 Jun 10. pii: btw325.

CRISPR-DO 0.1 – Genome-wide CRISPR Design and Optimization

CRISPR-DO 0.1

:: DESCRIPTION

CRISPR-DO is a web application for the Design and Optimization of guide sequences in several genomes (human, mouse, fly, worm and zebrafish). CRISPR-DO integrates an sgRNA efficiency prediction model (Xu, et al., 2015) and an off-target scoring function (Hsu, et al., 2013), which allow the users to evaluate the “goodness” of an sgRNA in both sensitivity and specificity.

::DEVELOPER

CRISPR-DO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux /MacOsX
  • Python

:: DOWNLOAD

 CRISPR-DO

:: MORE INFORMATION

Citation:

CRISPR-DO for genome-wide CRISPR design and optimization.
Ma J, Köster J, Qin Q, Hu S, Li W, Chen C, Cao Q, Wang J, Mei S, Liu Q, Xu H, Liu XS.
Bioinformatics. 2016 Jul 10. pii: btw476.

MetaBAT 0.26.3 – Reconstructing Single Genomes from Complex Microbial Communities

MetaBAT 0.26.3

:: DESCRIPTION

MetaBAT is an efficient tool for accurately reconstructing single genomes from complex microbial communities.

::DEVELOPER

Zhong Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX
  • C++ Compiler

:: DOWNLOAD

 MetaBAT

:: MORE INFORMATION

Citation

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities.
Kang DD, Froula J, Egan R, Wang Z.
PeerJ. 2015 Aug 27;3:e1165. doi: 10.7717/peerj.1165.

GHap 1.2.1 – Genome-Wide Haplotyping

GHap 1.2.1

:: DESCRIPTION

The GHap R package was designed to call haplotypes from phased marker data.

::DEVELOPER

Yuri Tani Utsunomiya<ytutsunomiya at gmail.com>, Marco Milanesi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

  GHap

:: MORE INFORMATION

Citation

GHap: An R package for Genome-wide Haplotyping.
Utsunomiya YT, Milanesi M, Utsunomiya AT, Ajmone-Marsan P, Garcia JF.
Bioinformatics. 2016 Jun 9. pii: btw356.

Pathoscope 2.0.6 / Clinical PathoScope 1.0.4 – Species Identification and Strain Attribution with Unassembled Sequencing data

Pathoscope 2.0.6  / Clinical PathoScope 1.0.4

:: DESCRIPTION

Pathoscope takes a next-generation sequencing reads from a mixture sample of multiple strains of genomes and it predicts which genomes potentially belongs there. Different from most of approach including composition method or similarity search with a daunting task of de novo assembly, the software applies the propagation of evidence in the Bayesian framework to an initial alignment result and reassign an correct membership of mapping by using the expectation and maximization algorithm.

Clinical Pathoscope is a program to identify pathogens/commensals/contaminants in unassembled sequencing reads.

::DEVELOPER

W. Evan Johnson Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Pathoscope / Clinical PathoScope

:: MORE INFORMATION

Citation

PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples.
Hong C, Manimaran S, Shen Y, Perez-Rogers JF, Byrd AL, Castro-Nallar E, Crandall KA, Johnson WE.
Microbiome. 2014 Sep 5;2:33. doi: 10.1186/2049-2618-2-33.

Genome Res. 2013 Oct;23(10):1721-9. doi: 10.1101/gr.150151.112.
Pathoscope: Species identification and strain attribution with unassembled sequencing data.
Francis OE, Bendall M, Manimaran S, Hong C, Clement NL, Castro-Nallar E, Snell Q, Schaalje GB, Clement MJ, Crandall KA, Johnson WE.

BMC Bioinformatics. 2014 Aug 4;15:262. doi: 10.1186/1471-2105-15-262.
Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data.
Byrd AL, Perez-Rogers JF, Manimaran S, Castro-Nallar E, Toma I, McCaffrey T, Siegel M, Benson G, Crandall KA1, Johnson WE.

miRNAFold – Ab initio miRNA Precursor Search in Genomes

miRNAFold

:: DESCRIPTION

miRNAFold is a fast ab-initio algorithm for searching for pre-miRNA precursors in genomes.

::DEVELOPER

EVRY RNA – IBISC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

miRNAFold: a web server for fast miRNA precursor prediction in genomes.
Tav C, Tempel S, Poligny L, Tahi F.
Nucleic Acids Res. 2016 May 29. pii: gkw459.

Nucleic Acids Res. 2012 Jun;40(11):e80. doi: 10.1093/nar/gks146. Epub 2012 Feb 22.
A fast ab-initio method for predicting miRNA precursors in genomes.
Tempel S1, Tahi F.

GMOL 2 – 3D Genome Structure Visualization

GMOL 2

:: DESCRIPTION

GMOL is an application designed to visualize genome structure in 3D. It allows users to view the genome structure at multiple scales, including: global, chromosome, loci, fiber, nucleosome, and nucleotide.

::DEVELOPER

Dr. Jianlin Cheng’s Bioinformatics and Systems Biology Laboratory

:: SCREENSHOTS

GMOL

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 GMOL

:: MORE INFORMATION

Gen3D – 3D Genome and Chromosome Structural Model Construction

Gen3D

:: DESCRIPTION

Gen3D is an application designed to determine three-dimensional genome and chromosome models. It uses chromosomal contact data to construct three-dimensional conformations.

::DEVELOPER

Dr. Jianlin Cheng’s Bioinformatics and Systems Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 Gen3D

:: MORE INFORMATION

Citation

Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data.
Nowotny J, Ahmed S, Xu L, Oluwadare O, Chen H, Hensley N, Trieu T, Cao R, Cheng J.
BMC Bioinformatics. 2015 Oct 23;16(1):338.

PheGenEx 3.0 – Phenome-Genome Explorer

PheGenEx 3.0

:: DESCRIPTION

PheGenEx is a realtime webtool for prediction, network-based analysis and visualization of phenotype-gene associations in the context of human diseases.

::DEVELOPER

KUANG LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  rcNet

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Oct 1;27(19):2692-9. doi: 10.1093/bioinformatics/btr463. Epub 2011 Aug 8.
Inferring disease and gene set associations with rank coherence in networks.
Hwang T1, Zhang W, Xie M, Liu J, Kuang R.