Ultra fast genome analysis

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An open-source dashboard web application providing an insightful overview of large, non-human-readable BAM files and enabling users to further analyze their alignments, all in real time.

Using recent advances in core web technologies (HTML5), we developed Scribl, a flexible genomic visualization library specifically targeting coordinate-based data such as genomic features, DNA sequence and genetic variants.

Scotty is an interactive web-based application that assists biologists to design an experiment with an appropriate sample size and read depth to satisfy the user-defined experimental objectives.

The 1000 Genomes Project was launched as one of the largest distributed data collection and analysis projects ever undertaken in biology, and members of the project data coordination center have developed and deployed several tools to enable widespread data access.

ART is a set of simulation tools that generate synthetic next-generation sequencing reads.

This study significantly contributes to the annotation of the unique cytoskeleton of Apicomplexa.

By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing.

This study demonstrates that exonic sequencing datasets, collected both in population based and medical sequencing projects, will be a useful substrate for detecting genic CNV events, particularly deletions.

The phenotype of a Toxoplasma gondii conditional mutant impaired in host cell invasion and egress was pinpointed to a defect in secretion of the micronemes, an apicomplexan-specific organelle that contains adhesion proteins.

This study represents a large step toward detecting and interpreting low frequency coding variation, clearly lays out technical steps for effective analysis of DNA capture data, and articulates functional and population properties of this important class of genetic variation.

VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API.

Here we present a comprehensive map of 7,380 MEI polymorphisms from the 1000 Genomes Project whole-genome sequencing data of 185 samples in three major populations detected with two detection methods.

We examined the joint allele frequency distributions across continental human populations and present an approach for combining complementary aspects of whole-genome, low-coverage data and targeted high-coverage data.

We present the first direct comparative analysis of male and female germline mutation rates from the complete genome sequences of two parent-offspring trios.

Introduction of a software suite for research analysis and data management using BAM files.

We provide an improved methodology for measuring gene expression changes in evolutionary diverged species using RNA Seq, where experimental artifacts can mimic evolutionary effects.

This tutorial review focuses on the recent progress in this highly active field of research with an emphasis on covalent modifications of DNA.

Map of unbalanced SVs based on whole genome DNA sequencing.

A standard variation file format for human genome sequences.

This pilot phase of the 1000 Genomes Project is designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms.

Our approach makes ~1000 genes accessible to genetic studies of disease association.

The Sequence Alignment/Map format and SAMtools.

Application of the Roche/454 platform to survey natural variation in strains of Drosophila melanogaster.

Mutational profiling with next-generation DNA sequencers.

A next-generation sequence assembly viewer program.

Whole-genome SNP calling in Illumina reads.

A base caller program for 454 reads.

Missing SNPs because of heterozygosity in PCR primer binding sites.

We simulated 1000 haplotypes using the standard coalescent for three world populations and applied three classes of block partitioning algorithms, assessing algorithm differences in number, size, and coverage of blocks inferred under different conditions of SNP density, allele frequency, and sample size.

The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations.

Sequence variations in the public human genome data reflect a bottlenecked population history.

STRP screening sets for the human genome at 5 cM density.

Human diallelic insertion/deletion polymorphisms. American Journal of Human Genetics.

Computational SNP discovery in DNA sequence data.

Single-nucleotide polymorphisms in the public domain: how useful are they?

A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms.

A general approach to single-nucleotide polymorphism discovery.

Sequence assembly with CAFTOOLS.