The variant call format (VCF) is a generic format for storing DNA polymorphism data such as
SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is …

ART is a set of simulation tools that generate synthetic next-generation sequencing reads.
This functionality is essential for testing and benchmarking tools for next-generation …

Genomic structural variants (SVs) are abundant in humans, differing from other forms of
variation in extent, origin and functional impact. Despite progress in SV characterization, the …

Motivation: Analysis of genomic sequencing data requires efficient, easy-to-use access to
alignment results and flexible data management tools (eg filtering, merging, sorting, etc.). …

Previously reported applications of the 454 Life Sciences pyrosequencing technology have
relied on deep sequence coverage for accurate polymorphism discovery because of …

The incomplete identification of structural variants (SVs) from whole-genome sequencing
data limits studies of human genetic diversity and disease association. Here, we apply a suite …

High-throughput sequencing technology enables population-level surveys of human genomic
variation. Here, we examine the joint allele frequency distributions across continental …

Single-nucleotide polymorphisms (SNPs) are the most abundant form of human genetic
variation and a resource for mapping complex genetic traits 1. The large volume of data …

Massively parallel sequencing instruments enable rapid and inexpensive DNA sequence
data production. Because these instruments are new, their data require characterization with …

SpeedSeq is an open-source genome analysis platform that accomplishes alignment, variant
detection and functional annotation of a 50× human genome in 13 h on a low-cost server …