LII:Next Generation Sequencing (NGS)/Integrative platforms
Introduction
[edit | edit source]- Open-source integrative platforms allow bioinformatics novice to carry out computationally intensive analyses online (either in public server or in private cloud).
- Numerous modules encompassing reads mapping, variant discovery, differential expression analysis and visualization are available. These tools also ensure transparency and reproducibility by recording every analysis metadata, including the tools, versions and parameters setting used during analysis.
- These platforms do not automate the entire analysis procedure and can be useful only if one is aware of what assumptions (e.g. the rationales behind the parameter choice) are being made. Note that these platforms may not necessarily be the best choice for many of the questions one is addressing. Users should also resort to the original release sites if the latest version of respective tools is needed.
Examples of integrative platforms
[edit | edit source]InsilicoDB
[edit | edit source]https://insilicodb.org/
The smart way to manage genomics data. Export genomics datasets to your favorite analysis tools.
Gene Pattern
[edit | edit source]http://www.broadinstitute.org/cancer/software/genepattern/
GenePattern is a powerful genomic analysis platform that provides access to more than 240 tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.
Galaxy
[edit | edit source]http://usegalaxy.org/
Galaxy is an open, web-based platform for data intensive biomedical research. Whether on this free public server or your own instance, you can perform, reproduce, and share complete analyses.
Gene Talk
[edit | edit source]https://www.gene-talk.de
GeneTalk is a web-based expert platform for analysis and interpretation of NGS data. Scientists and clinicians can filter variant call files (*.vcf) and reduce the amount of data. For diagnosis and interpretation of the data users can communicate, share data, and provide expertise to others via the platform.
GeneProf
[edit | edit source]http://www.geneprof.org
GeneProf is a web-based, bioinformatics software suite for the analysis of functional genomics experiments, e.g. RNA-seq or ChIP-seq. GeneProf supports integrated analyses of RNA-seq, ChIP-seq and other data generated using next-generation sequencing (NGS) platforms and provides a wealth of public data that can be easily compared with own results.
Basepair
[edit | edit source]www.basepairtech.com
Basepair is a SaaS platform for genomic data analysis that lets researchers quickly analyze raw data and choose among several high quality workflows from RNA-Seq, ChIP-Seq, DNA-Seq, etc.. Their cloud-based software significantly reduces turnaround time for scientists from weeks to hours without sacrificing quality.
Notes
This article is a direct transclusion of the Wikibooks article and therefore may not meet the same editing standards as LIMSwiki.
