Ehapp2: Estimate haplotype frequencies from pooled sequencing data with prior database information.

To reduce the cost of large-scale re-sequencing, multiple individuals are pooled together and sequenced called pooled sequencing. Pooled sequencing could provide a cost-effective alternative to sequencing individuals separately. To facilitate the application of pooled sequencing in haplotype-based diseases association analysis, the critical procedure is to accurately estimate haplotype frequencies from pooled samples.

Accurate estimation of haplotype frequency from pooled sequencing data and cost-effective identification of rare haplotype carriers by overlapping pool sequencing.

Motivation: A variety of hypotheses have been proposed for finding the missing heritability of complex diseases in genome-wide association studies. Studies have focused on the value of haplotype to improve the power of detecting associations with disease. To facilitate haplotype-based association analysis, it is necessary to accurately estimate haplotype frequencies of pooled samples.

Quantitative group testing-based overlapping pool sequencing to identify rare variant carriers.

Background: Genome-wide association studies have revealed that rare variants are responsible for a large portion of the heritability of some complex human diseases. This highlights the increasing importance of detecting and screening for rare variants. Although the massively parallel sequencing technologies have greatly reduced the cost of DNA sequencing, the identification of rare variant carriers by large-scale re-sequencing remains prohibitively expensive because of the huge challenge of constructing libraries for thousands of samples.

Intrinsic correlation of oligonucleotides: a novel genomic signature for metagenome analysis.

Because a vast majority (99%) of microbes in a given community is likely to be non-cultivable, metagenomics has gradually entered the mainstream of microbial research methods. With the development of high-throughput sequencing techniques, an increasing number of sequencing read data sets of metagenomes from various microbial communities have become available. For these data sets, metagenomic analysis based on mapping reads to microbial genomes has been hampered by the limited number of microbial genomes that are available.

Identifying rare variants with optimal depth of coverage and cost-effective overlapping pool sequencing.

Genome-wide association studies have identified hundreds of genetic variants associated with complex diseases although most variants identified so far explain only a small proportion of heritability, suggesting that rare variants are responsible for missing heritability. Identification of rare variants through large-scale resequencing becomes increasing important but still prohibitively expensive despite the rapid decline in the sequencing costs. Nevertheless, group testing based overlapping pool sequencing in which pooled rather than individual samples are sequenced will greatly reduces the efforts of sample preparation as well as the costs to screen for rare variants.

Genome analysis and signature discovery for diving and sensory properties of the endangered Chinese alligator.

Crocodilians are diving reptiles that can hold their breath under water for long periods of time and are crepuscular animals with excellent sensory abilities. They comprise a sister lineage of birds and have no sex chromosome. Here we report the genome sequence of the endangered Chinese alligator (Alligator sinensis) and describe its unique features.