Next Generation Sequencing Resources

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SeqAnswer

A discussion forum for the Next Generation Sequencing community. If you have a question about NGS, they probably have many answers.
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WIKI2: List of RNA-Seq Bioinformatics Tools

By far the most comprehensive Bioinformatics Tools for RNA-seq analysis
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GenomeSpace

GenomeSpace is a cloud-based interoperability framework to support integrative genomics analysis through an easy-to-use Web interface
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RNA-seqlopedia

Very cool resource for learning all about RNAseq
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Wikipedia: List of RNA-seq Bioinformatics Tools

A collection of bioinformatics tools for RNA-seq analysis
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Tutorial: RNA-seq differential expression & pathway analysis with Sailfish, DESeq2, GAGE, and Pathview

Very nice R script to do RNA-seq Analysis. A PDF version can be found here
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NGS De novo assembly

A good wikibooks link for a comprehensive document on NGS De novo assembly
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GitHub: RNA-seq Tutorials

This is a very good resource for season informatics who are not afraid to work on the command line interface
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Designing you NGS Run

A general NGS sequencing depth info
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Recount

A multi-experiment resource of analysis-ready RNA-seq gene and exon count dataset