Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies

A Comprehensive Transcriptome Assembly of Pigeonpea (Cajanus cajan L.) using Sanger and Second-Generation Sequencing Platforms

(2012) Himabindu Kudapa et al.   Molecular Plant

Subgroup-specific structural variation across 1,000 medulloblastoma genomes

(2012) Paul A. Northcott et al.   NATURE

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample

(2012) Chengwei Luo et al.   PLoS One

Addressing challenges in the production and analysis of illumina sequencing data

(2011) Martin Kircher et al.   BMC GENOMICS

Accurate and comprehensive sequencing of personal genomes

(2011) S. S. Ajay et al.   GENOME RESEARCH

Technology-specific error signatures in the 1000 Genomes Project data

(2011) Michael Nothnagel et al.   HUMAN GENETICS

Performance comparison of whole-genome sequencing platforms

(2011) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

Systematic bias in high-throughput sequencing data and its correction by BEADS

(2011) Ming-Sin Cheung et al.   NUCLEIC ACIDS RESEARCH

Comparison of Sequence Reads Obtained from Three Next-Generation Sequencing Platforms

(2011) Shingo Suzuki et al.   PLoS One

Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions

(2011) Weixin Wang et al.   Scientific Reports

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Advances in understanding cancer genomes through second-generation sequencing

(2010) Matthew Meyerson et al.   NATURE REVIEWS GENETICS

Diversity of Human Copy Number Variation and Multicopy Genes

(2010) Peter H. Sudmant et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores

(2009) Rafael A Irizarry et al.   NATURE GENETICS

Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

(2009) R. Drmanac et al.   SCIENCE

De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data

(2009) Scott DiGuistini et al.   GENOME BIOLOGY