Performance comparison of benchtop high-throughput sequencing platforms

The Sequence Alignment/Map format and SAMtools

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Fast and accurate short read alignment with Burrows-Wheeler transform

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Sequencing technologies – the next generation

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Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities

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Accurate whole human genome sequencing using reversible terminator chemistry

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Epidemic Profile of Shiga-Toxin–Producing Escherichia coli O104:H4 Outbreak in Germany

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Tablet-next generation sequence assembly visualization.

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Genome engineering using the CRISPR-Cas9 system

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Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies.

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Coming of age: ten years of next-generation sequencing technologies

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The sequence of sequencers: The history of sequencing DNA

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Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

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Characterizing and measuring bias in sequence data

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Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing

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Towards a genomics-informed, real-time, global pathogen surveillance system

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The promise and challenge of high-throughput sequencing of the antibody repertoire

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Sequence assembly demystified

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High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology

Ercolini, D. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.00256-13 · Cited by 479

Historical perspective, development and applications of next-generation sequencing in plant virology

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Microbiome of Pacific Whiteleg shrimp reveals differential bacterial community composition between Wild, Aquacultured and AHPND/EMS outbreak conditions

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A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome

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Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis

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Bacterial diversity and composition of alfalfa silage as analyzed by Illumina MiSeq sequencing: Effects of Escherichia coli O157:H7 and silage additives

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Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis

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Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data

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Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study

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STR allele sequence variation: Current knowledge and future issues

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Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires

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Detecting and correcting systematic variation in large-scale RNA sequencing data

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Review of applications of high-throughput sequencing in personalized medicine: barriers and facilitators of future progress in research and clinical application

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Is DNA Barcoding Actually Cheaper and Faster than Traditional Morphological Methods: Results from a Survey of Freshwater Bioassessment Efforts in the United States?

Stein, E. D., Martinez, M. C., Stiles, S., Miller, P. E., & Zakharov, E. V. (2014) · PLoS ONE · doi:10.1371/journal.pone.0095525 · Cited by 152

High Throughput Sequencing for Detection of Foodborne Pathogens

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Clonal relationships of CSF B cells in treatment-naive multiple sclerosis patients

Eggers, E. L., Michel, B. A., Wu, H., Wang, S.-Z., Bevan, C. J., Abounasr, A., Pierson, N. S., Bischof, A., Kazer, M., Leitner, E., et al. (2017) · JCI Insight · doi:10.1172/jci.insight.92724 · Cited by 93

Genes, behavior and next‐generation RNA sequencing

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Human Genome Sequencing at the Population Scale: A Primer on High-Throughput DNA Sequencing and Analysis

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Next-generation sequencing as an approach to dairy starter selection

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Allelic Imbalance in Regulation of ANRIL through Chromatin Interaction at 9p21 Endometriosis Risk Locus

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Rapid Diagnosis of Lower Respiratory Infection using Nanopore-based Clinical Metagenomics

Charalampous, T., Richardson, H., Kay, G. L., Baldan, R., Jeanes, C., Rae, D., Grundy, S., Turner, D. J., Wain, J., Leggett, R. M., et al. (2018) · doi:10.1101/387548 · Cited by 37

Reply to ‘Errors in long-read assemblies can critically affect protein prediction’

Koren, S., Phillippy, A. M., Simpson, J. T., Loman, N. J., & Loose, M. (2019) · Nature Biotechnology · doi:10.1038/s41587-018-0005-y · Cited by 30

Phylotranscriptomics suggests the jawed vertebrate ancestor could generate diverse helper and regulatory T cell subsets

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Single-Cell Semiconductor Sequencing

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Pervasive transcription of the mitochondrial genome in Candida albicans is revealed in mutants lacking the mtEXO RNase complex

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