We developed most reliable and advanced pipelines to analyze next generation sequencing data. These pipelines have tools which are recently published and cited in good quality journals. Below are some of the tools which are used individually or within our pipelines.
The program uses an array of bioinformatics tools, which include publicly available, in-house developed and proprietary ones. A list of some of the bioinformatic tools are provided below. The list will be continuously updated to add more tools. LSUHSC investigators are welcome to use these tools independently or with support from BIG staff. However, all investigators using these tools listed on this website must acknowledge and cite the original sources appropriately.
Genepattern: The program provides hundreds of analytical tools for the analysis of gene expression (RNA-seq and microarray), sequence variation and copy number, proteomic, flow cytometry, and network analysis. These tools are all available through a web interface with no programming experience required or with assistance from BIG staff. Genepattern is available for use through our Bioinformatics and Computational Genomics Lab or through the web at this site: http://www.broadinstitute.org/cancer/software/genepattern/
Pomelo II: This is web-based bioinformatics software for analysis of gene expression data. The software is all available through a web interface with no programming experience required or with assistance from BIG staff. Pomelo II is available for use through our Bioinformatics and Computational Genomics Lab or through the web at this site: http://pomelo2.iib.uam.es/
GENE-E: GENE-E is a matrix visualization and analysis platform designed to support visual data exploration. It includes heat map, clustering, filtering, charting, marker selection, and many other tools. In addition to supporting generic matrices, GENE-E also contains tools that are designed specifically for genomics data. GENE-E was created and is developed by Joshua Gould. When referencing your use of GENE-E, please cite this website. http://www.broadinstitute.org/cancer/softwareGENE-E/
GATK: The Genome Analysis Toolkit or GATK is a software package for analysis of high-throughput sequencing data, developed by the Data Science and Data Engineering group at the Broad Institute. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. https://www.broadinstitute.org/gatk/
GenomeSpace is a cloud-based interoperability framework to support integrative genomics analysis through an easy-to-use Web interface. GenomeSpace provides access to a diverse range of bioinformatics tools, and bridges the gaps between the tools, making it easy to leverage the available analyses and visualizations in each of them. The tools retain their native look and feel, with GenomeSpace providing frictionless conduits between them through a lightweight interoperability layer. GenomeSpace does not perform any analyses itself; these are done within the member tools wherever they live – desktop, Web service, cloud, in-house server, etc. Rather, GenomeSpace provides tool selection and launch capabilities, and acts as a data highway automatically reformatting data as required when results move from the output of one tool to input for the next. http://www.genomespace.org/
Haploview: The program is designed to facilitate the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. https://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/haploview
Genome Browser: It is useful software for navigating the genomes. The software can be accessed via the UCSC Genome Browser website: https://genome.ucsc.edu/.
Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations: https://www.broadinstitute.org/igv/.
Integrated Genome Browser (IGB) is a fast, free, and highly customizable genome browser you can use to view and explore big genomic datasets. IGB runs on your desktop and can load data from your local files and also from the internet. http://bioviz.org/igb/index.html
1000 Genomes Project:The 1000 Genomes Project is a public resource which ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. As the project ended, the Data Coordination Centre at EMBL-EBI has received continued funding from the Wellcome Trust to maintain and expand the resource. The International Genome Sample Resource (IGSR) was set up to do this. It is powered by the 1000 Genomes Browser, a genome navigation tool for browsing the genomes in the 1000 Genome Project: The project can be accessed via the following browser: http://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/