Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicine

De novo genome assembly: what every biologist should know

(2012) Monya Baker   NATURE METHODS

SIMPLEX: Cloud-Enabled Pipeline for the Comprehensive Analysis of Exome Sequencing Data

(2012) Maria Fischer et al.   PLoS One

Base-calling for next-generation sequencing platforms

(2011) C. Ledergerber et al.   BRIEFINGS IN BIOINFORMATICS

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

(2011) I. Pagani et al.   NUCLEIC ACIDS RESEARCH

An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System

(2010) Brian D. Ondov et al.   BIOINFORMATICS

Recent progress and new challenges in metagenomics for biotechnology

(2010) Ludmila Chistoserdova   BIOTECHNOLOGY LETTERS

A survey of sequence alignment algorithms for next-generation sequencing

(2010) H. Li et al.   BRIEFINGS IN BIOINFORMATICS

Single molecule linear analysis of DNA in nano-channel labeled with sequence specific fluorescent probes

(2010) S. K. Das et al.   NUCLEIC ACIDS RESEARCH

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing

(2009) Nathan L. Clement et al.   BIOINFORMATICS

De novo transcriptome assembly with ABySS

(2009) I. Birol et al.   BIOINFORMATICS

Updates to the RMAP short-read mapping software

(2009) A. D. Smith et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Next-Generation Sequencing: From Basic Research to Diagnostics

(2009) K. V. Voelkerding et al.   CLINICAL CHEMISTRY

BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing

(2009) W.-C. Kao et al.   GENOME RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Personalized copy number and segmental duplication maps using next-generation sequencing

(2009) Can Alkan et al.   NATURE GENETICS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Next-generation DNA sequencing techniques

(2009) Wilhelm J. Ansorge   New Biotechnology

BFAST: An Alignment Tool for Large Scale Genome Resequencing

(2009) Nils Homer et al.   PLoS One

SHRiMP: Accurate Mapping of Short Color-space Reads

(2009) Stephen M. Rumble et al.   PLoS Computational Biology

Simultaneous alignment of short reads against multiple genomes

(2009) Korbinian Schneeberger et al.   GENOME BIOLOGY

Improved base calling for the Illumina Genome Analyzer using machine learning strategies

(2009) Martin Kircher et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

ZOOM! Zillions of oligos mapped

(2008) H. Lin et al.   BIOINFORMATICS

Slider--maximum use of probability information for alignment of short sequence reads and SNP detection

(2008) N. Malhis et al.   BIOINFORMATICS

SeqMap: mapping massive amount of oligonucleotides to the genome

(2008) H. Jiang et al.   BIOINFORMATICS

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

Probabilistic base calling of Solexa sequencing data

(2008) Jacques Rougemont et al.   BMC BIOINFORMATICS

Sequencing of natural strains of Arabidopsis thaliana with short reads

(2008) S. Ossowski et al.   GENOME RESEARCH

ALLPATHS: De novo assembly of whole-genome shotgun microreads

(2008) J. Butler et al.   GENOME RESEARCH

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Alta-Cyclic: a self-optimizing base caller for next-generation sequencing

(2008) Yaniv Erlich et al.   NATURE METHODS