Reliable Identification of Genomic Variants from RNA-Seq Data

The Sequence Alignment/Map format and SAMtools

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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

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TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.

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<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool

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A map of human genome variation from population-scale sequencing.

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Alternative isoform regulation in human tissue transcriptomes

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Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

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Accurate whole human genome sequencing using reversible terminator chemistry

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Integrating common and rare genetic variation in diverse human populations

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The clonal and mutational evolution spectrum of primary triple-negative breast cancers

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The Diploid Genome Sequence of an Individual Human

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Evolution and functional impact of rare coding variation from deep sequencing of human exomes

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Personal omics profiling reveals dynamic molecular and medical phenotypes

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Understanding mechanisms underlying human gene expression variation with RNA sequencing

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MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

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A survey of sequence alignment algorithms for next-generation sequencing

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Transcriptome genetics using second generation sequencing in a Caucasian population

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Mechanisms and consequences of widespread random monoallelic expression

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Comment on “Widespread RNA and DNA Sequence Differences in the Human Transcriptome”

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G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

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RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues

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Tools and best practices for data processing in allelic expression analysis.

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Next Generation Sequencing (NGS): A Revolutionary Technology in Pharmacogenomics and Personalized Medicine in Cancer

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Single suture craniosynostosis: Identification of rare variants in genes associated with syndromic forms

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