EuGene-PP 1.3 – Next Generation Automated Annotation Pipeline for Prokaryotic Genomes

EuGene-PP 1.3

:: DESCRIPTION

EuGene-PP (Prokaryote Pipeline) facilitates the application of EuGene on prokaryotic genomes, integrating any type of oriented gene expression information (RNA-seq or Tilling arrays, supporting all usual file formats), protein similarities, output of existing CDS and ncRNA predictors, and statistical information.

::DEVELOPER

EuGene team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 EuGene-PP

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 30. pii: btu366. [Epub ahead of print]
EuGene-PP: A Next Generation Automated Annotation Pipeline for Prokaryotic Genomes.
Sallet E1, Gouzy J2, Schiex T

SPANDx 3.2 – Comparative Analysis of Haploid Next-generation Re-sequencing data

SPANDx 3.2

:: DESCRIPTION

SPANDx (Synergised Pipeline for Analysis of NGS Data in Linux) is a versatile and customisable tool for the processing of large NGS datasets from raw reads to comparative analysis into a single tool.

::DEVELOPER

Dr Derek Sarovich

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SPANDx

:: MORE INFORMATION

Citation

BMC Res Notes. 2014 Sep 8;7:618. doi: 10.1186/1756-0500-7-618.
SPANDx: a genomics pipeline for comparative analysis of large haploid whole genome re-sequencing datasets.
Sarovich DS1, Price EP.

GATK 3.8-0 – Analysis Tools for Next-generation DNA Sequencers

GATK 3.8-0

:: DESCRIPTION

GATK (The Genome Analysis Toolkit) is a structured programming framework designed to enable the rapid development of efficient and robust analysis tools for next-generation DNA sequencers. The GATK solves the data management challenge by separating data access patterns from analysis algorithms, using the functional programming philosophy of Map/Reduce. Since the GATK’s traversal engine encapsulates the complexity of efficiently accessing the next-generation sequencing data, researchers and developers are free to focus on their specific analysis algorithms. This not only vastly improves the productivity of developers, who can quickly write new analyses, but also results in tools that are efficient and robust, and can benefit from improvements to a common data management engine.

::DEVELOPER

The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

GATK

:: MORE INFORMATION

Citation

Depristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, Del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ.
A framework for variation discovery and genotyping using next-generation DNA sequencing data
Nature Genetics 43, 491–498 (2011) doi:10.1038/ng.806

SpliceSeq 2.1 – Investigate alternative mRNA Splicing in Next Generation mRNA Sequence data

SpliceSeq 2.1

:: DESCRIPTION

SpliceSeq provides a quick, easy method of investigating alternative mRNA splicing in next generation mRNA sequence data. The tool may be used on a single mRNA-Seq sample to identify genes with multiple spliceforms or on a pair of samples to identify differential splicing between the samples. Sequence reads are mapped to splice graphs that unambiguously quantify the inclusion level of each exon and splice junction. The graphs are then traversed to predict the protein isoforms that are likely to result from the observed exon and splice junction reads. UniProt annotations are mapped to each protein isoform to identify potential functional impacts of alternative splicing.

::DEVELOPER

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 SpliceSeq

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 15;28(18):2385-7. Epub 2012 Jul 20.
SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts.
Ryan MC, Cleland J, Kim R, Wong WC, Weinstein JN.

PANGEA 1.0.2 – Pipeline Analysis for Next GEneration Amplicons

PANGEA 1.0.2

:: DESCRIPTION

PANGEA is a code useful for the analysis of 16S rRNA nucleotide sequences

::DEVELOPER

University of Florida Genetics Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Perl

:: DOWNLOAD

 PANGEA

:: MORE INFORMATION

Citation

ISME J. 2010 Jul;4(7):852-61. doi: 10.1038/ismej.2010.16. Epub 2010 Feb 25.
PANGEA: pipeline for analysis of next generation amplicons.
Giongo A1, Crabb DB, Davis-Richardson AG, Chauliac D, Mobberley JM, Gano KA, Mukherjee N, Casella G, Roesch LF, Walts B, Riva A, King G, Triplett EW.

SEAStAR v0.4.18 – Analysis of Next-generation Metagenomes

SEAStAR v0.4.18

:: DESCRIPTION

SEAStAR is a package of open-source tools supporting the construction of analysis pipelines for environmental next-generation sequencing data.

::DEVELOPER

Armbrust Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 SEAStAR

:: MORE INFORMATION

GNUMAP 3.0.2 / GNUMAPS – Genomic Next-generation Universal MAPper

GNUMAP 3.0.2 / GNUMAPS

:: DESCRIPTION

The GNUMAP (Genomic Next-generation Universal MAPper) is a program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size. Currently, gnumap is designed to be used with the _int.txt data received from the Solexa/Illumina machine.

GNUMAPS is a user-friendly pipeline with a optimized version of GNUMAP. This pipeline supports DNA, RNA, any library type (unstranded or strand-specific reads), single-end, and paired-end, bisulfited sequence reads, and RNA-editing discovery feature. Note that we keep updating this pipeline.

::DEVELOPER

GNUMAP Team , W. Evan Johnson Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GNUMAP / GNUMAPS

:: MORE INFORMATION

Citation:

Clement NL, Snell Q, Clement MJ, Hollenhorst PC, Purwar J, Graves BJ, Cairns BR, Johnson WE
The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing
Bioinformatics (2010) 26 (1): 38-45.

GenomeView 2450 – Next-generation Genome Browser and Editor

GenomeView 2450

:: DESCRIPTION

GenomeView is a next-generation stand-alone genome browser and editor.It provides interactive visualization of sequences, annotation, multiple alignments, syntenic mappings, short read alignments and more. Many standard file formats are supported and new functionality can be added using a plugin system.

:DEVELOPER

Thomas Abeel, Broad Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Java

:: DOWNLOAD

 GenomeView

:: MORE INFORMATION

Citation

GenomeView: a next-generation genome browser
Thomas Abeel; Thomas Van Parys; Yvan Saeys; James Galagan; Yves Van de Peer
Nucleic Acids Research 2011; doi: 10.1093/nar/gkr995

GeneTerrain – Next-generation Panel Biomarker Discovery and Validation software

GeneTerrain

:: DESCRIPTION

GeneTerrain is a next-generation panel biomarker discovery and validation software.

::DEVELOPER

Discovery Informatics and Computing Laboratory@ Indiana University School of Informatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Please join the mailing group to obtain instructions for downloading a pre-release version of the software.

:: MORE INFORMATION

Citation

You Qian, Shiaofen Fang, and Jake Y. Chen (2008)
GeneTerrain: Visual Exploration of Differential Gene Expression Profiles Organized in Native Biomolecular Interaction Networks
Information Visualization, doi: 10.1057/palgrave.ivs.9500169