Improvement in detection of minor alleles in next generation sequencing by base quality recalibration

Declining transition/transversion ratios through time reveal limitations to the accuracy of nucleotide substitution models

(2015) Sebastián Duchêne et al.   BMC EVOLUTIONARY BIOLOGY

Extensive tissue-related and allele-related mtDNA heteroplasmy suggests positive selection for somatic mutations

(2015) Mingkun Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Next generation sequencing technology: Advances and applications

(2014) H.P.J. Buermans et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Extensive pathogenicity of mitochondrial heteroplasmy in healthy human individuals

(2014) K. Ye et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RACER: Rapid and accurate correction of errors in reads

(2013) Lucian Ilie et al.   BIOINFORMATICS

freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers

(2013) Gabriel Renaud et al.   BIOINFORMATICS

CrossMap: a versatile tool for coordinate conversion between genome assemblies

(2013) Hao Zhao et al.   BIOINFORMATICS

Discovering motifs that induce sequencing errors

(2013) Manuel Allhoff et al.   BMC BIOINFORMATICS

ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data

(2012) Christopher R Cabanski et al.   BMC BIOINFORMATICS

The effect of strand bias in Illumina short-read sequencing data

(2012) Yan Guo et al.   BMC GENOMICS

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Mitochondrial genomes gleaned from human whole-exome sequencing

(2012) Ernesto Picardi et al.   NATURE METHODS

Fidelity of capture-enrichment for mtDNA genome sequencing: influence of NUMTs

(2012) Mingkun Li et al.   NUCLEIC ACIDS RESEARCH

All your base: a fast and accurate probabilistic approach to base calling

(2012) Tim Massingham et al.   GENOME BIOLOGY

A new approach for detecting low-level mutations in next-generation sequence data

(2012) Mingkun Li et al.   GENOME BIOLOGY

Assemblathon 1: A competitive assessment of de novo short read assembly methods

(2011) D. Earl et al.   GENOME RESEARCH

naiveBayesCall: An Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing

(2011) Wei-Chun Kao et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study

(2011) Hiroki Goto et al.   GENOME BIOLOGY

Detecting Heteroplasmy from High-Throughput Sequencing of Complete Human Mitochondrial DNA Genomes

(2010) Mingkun Li et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Next Generation of Molecular Markers From Massively Parallel Sequencing of Pooled DNA Samples

(2010) Andreas Futschik et al.   GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Heteroplasmic mitochondrial DNA mutations in normal and tumour cells

(2010) Yiping He et al.   NATURE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) Martin Kircher et al.   GENOME BIOLOGY

A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing

(2008) Richard E. Green et al.   CELL