I am often asked for a good NGS reference, or references that explain the technology used in next generation sequencing experiments. I have gathered together a list of my favourites over the past few years and thought readers of this blog might like to see what I’d recommend. I would be very interested to hear if you think I should include other references and if so why.

General reviews:
Applications of next-generation sequencing technologies in functional genomics.
Finding the fifth base: genome-wide sequencing of cytosine methylation.
Whole-genome re-sequencing.
Next-generation DNA sequencing.
Sequencing technologies – the next generation.
The real cost of sequencing: higher than you think!
Sequence census methods for functional genomics.

Cancer genomics: 
Cancer genome sequencing: a review.
Next-generation sequencing.
Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing.
A comprehensive catalogue of somatic mutations from a human cancer genome.
A small-cell lung cancer genome with complex signatures of tobacco exposure.

Illumina sequencing:
Accurate whole human genome sequencing using reversible terminator chemistry.
A large genome center’s improvements to the Illumina sequencing system.
Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. 
Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study.

Ion Torrent sequencing:
An integrated semiconductor device enabling non-optical genome sequencing.
A Torrent of data: mapping chromatin organization using 5C and high-throughput sequencing.
Performance comparison of benchtop high-throughput sequencing platforms

Roche/454 sequencing:
Genome sequencing in microfabricated high-density picolitre reactors.The complete genome of an individual by massively parallel DNA sequencing

Mapping and quantifying mammalian transcriptomes by RNA-Seq.
Transcriptome sequencing to detect gene fusions in cancer.
RNA-Seq: a revolutionary tool for transcriptomics.
Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes.
Is sequencing enlightenment ending the dark age of the transcriptome?
Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells.
Comprehensive comparative analysis of strand-specific rnA sequencing methods

High-resolution profiling of histone methylations in the human genome.
FOXA1 is a key determinant of estrogen receptor function and endocrine response.
Genome-wide mapping of in vivo protein–DNA interactions.
Applications of next-generation sequencing technologies in functional genomics. Genomics.
ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions.
Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding Science.

Genome capture:
Target-enrichment strategies for next-generation sequencing.
Exome sequencing as a tool for Mendelian disease gene discovery.
Carrier Testing for Severe Childhood Recessive Diseases by Next-Generation Sequencing
Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA.