From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

(2012) Andreas Wilm et al.   NUCLEIC ACIDS RESEARCH

Complete mitochondrial DNA genome sequences from the first New Zealanders

(2012) M. Knapp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

High-throughput DNA sequencing - concepts and limitations

(2010) Martin Kircher et al.   BIOESSAYS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets

(2010) Robert Schmieder et al.   BMC BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

Mitochondrial DNA Variant Discovery and Evaluation in Human Cardiomyopathies through Next-Generation Sequencing

(2010) Michael V. Zaragoza et al.   PLoS One

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

Toward next-generation sequencing of mitochondrial genomes — Focus on parasitic worms of animals and biotechnological implications

(2009) Aaron R. Jex et al.   BIOTECHNOLOGY ADVANCES

A comprehensive catalogue of somatic mutations from a human cancer genome

(2009) Erin D. Pleasance et al.   NATURE

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

An integrated pipeline for next-generation sequencing and annotation of mitochondrial genomes

(2009) A. R. Jex et al.   NUCLEIC ACIDS RESEARCH

Harnessing genomics for evolutionary insights

(2009) Antonis Rokas et al.   TRENDS IN ECOLOGY & EVOLUTION

Next generation sequence analysis for mitochondrial disorders

(2009) Valeria Vasta et al.   Genome Medicine

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

(2008) Richard E. Green et al.   CELL

Sequence assembly

(2008) K. Scheibye-Alsing et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

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

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

Pyrobayes: an improved base caller for SNP discovery in pyrosequences

(2008) Aaron R Quinlan et al.   NATURE METHODS

Parallel tagged sequencing on the 454 platform

(2008) Matthias Meyer et al.   Nature Protocols