cis-X v1.4.0 – Search for Activating Regulatory Variants in the Tumor Genome

cis-X v1.4.0

:: DESCRIPTION

cis-X is a new computational method for the discovery of noncoding regulatory variants in individual cancer genomes that will cause cis-activation of target gene transcription.

::DEVELOPER

Zhang (Jinghui Zhang) Lab,St. Jude Children’s Research Hospital

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

cis-X

:: MORE INFORMATION

SILP2 – ILP-based Maximum Likelihood Genome Scaffolding

SILP2

:: DESCRIPTION

SILP2 is a stand-alone scaffolding tool that generates maximum likelihood scaffolds via integer linear programming (ILP). SILP2 achieves high scalability without sacrificing optimality by solving the large ILP formulations required to scaffold mammalian-size genomes via a non-serial dynamic programming (NSDP) approach based on decomposing the scaffolding graph into 3-connected components.

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SILP2

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2014;15 Suppl 9:S9. doi: 10.1186/1471-2105-15-S9-S9. Epub 2014 Sep 10.
ILP-based maximum likelihood genome scaffolding.
Lindsay J, Salooti H, Măndoiu I, Zelikovsky A.

Atlas2 1.4.3 / Atlas2Cloud 0.5 – Genome Analysis Suite

Atlas2 1.4.3 / Atlas2Cloud 0.5

:: DESCRIPTION

Atlas2 is a next-generation sequencing suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in Whole Exome Capture Sequencing (WECS) data.

Atlas2 Cloud is a framework for personal genome analysis in the cloud.

::DEVELOPER

Human Genome Sequencing Center, Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Atlas2 / Atlas2Cloud

:: MORE INFORMATION

Citation

Atlas2 Cloud: a framework for personal genome analysis in the cloud.
Evani US, Challis D, Yu J, Jackson AR, Paithankar S, Bainbridge MN, Jakkamsetti A, Pham P, Coarfa C, Milosavljevic A, Yu F.
BMC Genomics. 2012;13 Suppl 6:S19. doi: 10.1186/1471-2164-13-S6-S19. Epub 2012 Oct 26.

PBSuite 150824 – Software for Long-Read Sequencing Data from PacBio

PBSuite 150824

:: DESCRIPTION

PBSuite includes:
PBJelly – the genome upgrading tool.
PBHoney – the structural variation discovery tool

PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles.

PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp).

::DEVELOPER

Human Genome Sequencing Center, Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 PBSuite

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2014 Jun 10;15:180. doi: 10.1186/1471-2105-15-180.
PBHoney: identifying genomic variants via long-read discordance and interrupted mapping.
English AC1, Salerno WJ, Reid JG.

English AC, Richards S, Han Y, Wang M, Vee V, et al. (2012)
Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology.
PLoS ONE 7(11): e47768. doi:10.1371/journal.pone.0047768

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.

RPAN 0.91 – Rice Pan-genome Browser for 3K rice genomes

RPAN 0.91

:: DESCRIPTION

RPAN is a genome browser to search and visualize the rice pan-genome derived from 3K RGP. RPAN contains a database of the basic information of 3010 rice accessions, including genomic sequences, gene annotations, PAV information and gene expression data of the rice pan-genome. At least 12 000 novel genes absent in the reference genome were included. RPAN also provides multiple search and visualization functions. RPAN can be a rich resource for rice biology and rice breeding.

::DEVELOPER

Dr. Chaochun Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser / Linux with apache server.

:: DOWNLOAD

RPAN

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2017 Jan 25;45(2):597-605. doi: 10.1093/nar/gkw958. Epub 2016 Dec 10.
RPAN: rice pan-genome browser for ~3000 rice genomes.
Sun C et al.

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

SpeedSeq v0.1.2 – Framework for Rapid Genome Analysis and Interpretation

SpeedSeq v0.1.2

:: DESCRIPTION

SpeedSeq is an open-source genome analysis platform that accomplishes alignment, variant detection and functional annotation of a 50× human genome in 13 h on a low-cost server and alleviates a bioinformatics bottleneck that typically demands weeks of computation with extensive hands-on expert involvement.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

SpeedSeq

:: MORE INFORMATION

Citation:

Nat Methods. 2015 Oct;12(10):966-8. doi: 10.1038/nmeth.3505. Epub 2015 Aug 10.
SpeedSeq: ultra-fast personal genome analysis and interpretation.
C Chiang, R M Layer, G G Faust, M R Lindberg, D B Rose, E P Garrison, G T Marth, A R Quinlan, and I M Hall.

MeDuSa 1.6 – Multi-draft based Scaffolder

MeDuSa 1.6

:: DESCRIPTION

MeDuSa (Multi-Draft based Scaffolder) is a draft genome scaffolder that uses multiple reference genomes in a graph-based approach.

::DEVELOPER

Florence Computational Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • Java

:: DOWNLOAD

  MeDuSa

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Mar 25. pii: btv171.
MeDuSa: a multi-draft based scaffolder.
Bosi E, Donati B, Galardini M, Brunetti S, Sagot MF, Lió P, Crescenzi P, Fani R, Fondi M

SAGE 2 – String Graph Assembly of GEnomes

SAGE 2

:: DESCRIPTION

SAGE is a new string-overlap graph-based de novo genome assembler.

::DEVELOPER

LUCIAN ILIE

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SAGE

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Sep 15;15:302. doi: 10.1186/1471-2105-15-302.
SAGE: String-overlap Assembly of GEnomes.
Ilie L1, Haider B, Molnar M, Solis-Oba R.