SM a SH: a benchmarking toolkit for human genome variant calling

For better or worse, benchmarks shape a field

(2012) David Patterson   COMMUNICATIONS OF THE ACM

Next-generation sequencing data interpretation: enhancing reproducibility and accessibility

(2012) Anton Nekrutenko et al.   NATURE REVIEWS GENETICS

Genomes in a bottle: creating standard reference materials for genomic variation - why, what and how?

(2012) Justin M Zook et al.   GENOME BIOLOGY

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

(2011) D. Earl et al.   GENOME RESEARCH

Sequence-based characterization of structural variation in the mouse genome

(2011) Binnaz Yalcin et al.   NATURE

The new date, new format, new goals and new sponsor of the Archon Genomics X PRIZE Competition

(2011) Larry Kedes et al.   NATURE GENETICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

A Human Genome Structural Variation Sequencing Resource Reveals Insights into Mutational Mechanisms

(2010) Jeffrey M. Kidd et al.   CELL

Dindel: Accurate indel calls from short-read data

(2010) C. A. Albers et al.   GENOME RESEARCH

Integrating common and rare genetic variation in diverse human populations

(2010)   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Characterization of missing human genome sequences and copy-number polymorphic insertions

(2010) Jeffrey M Kidd et al.   NATURE METHODS

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 $1,000 genome, the $100,000 analysis?

(2010) Elaine R Mardis   Genome Medicine

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

(2009) Deanna M. Church et al.   PLOS BIOLOGY