Related papers: Sensitive Long-Indel-Aware Alignment of Sequencing…
Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate enormous amounts of…
Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads…
We present the Scalable Nucleotide Alignment Program (SNAP), a new short and long read aligner that is both more accurate (i.e., aligns more reads with fewer errors) and 10-100x faster than state-of-the-art tools such as BWA. Unlike recent…
Next-generation sequencing techniques have facilitated a large scale analysis of human genetic variation. Despite the advances in sequencing speeds, the computational discovery of structural variants is not yet standard. It is likely that…
Aligning millions of short DNA or RNA reads, of 75 to 250 base pairs each, to a reference genome is a significant computation problem in bioinformatics. We present a flexible and fast FPGA-based short read alignment tool. Our aligner makes…
The rapidly changing landscape of sequencing technologies brings new opportunities to genomics research. Longer sequence reads and higher sequence throughput coupled with ever-improving base accuracy and decreasing per-base cost is now…
(An updated version of this manuscript has been accepted to Scientific Reports in 2016, please refer to http://www.nature.com/articles/srep31900) The highly anticipated transition from next generation sequencing (NGS) to third generation…
We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers. While long sequences of DNA offer enormous…
Motivation: Detection of structural variants (SV) from the alignment of sample DNA reads to the reference genome is an important problem in understanding human diseases. Long reads that can span repeat regions, along with an accurate…
Motivation: Next generation methods of DNA sequencing produce relatively high rate of reading errors, which interfere with de novo genome assembly of newly sequenced organisms and particularly affect the quality of SNP detection important…
To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the…
DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics.…
The detection of genomic structural variation (SV) has advanced tremendously in recent years due to progress in high-throughput sequencing technologies. Novel sequence insertions, insertions without similarity to a human reference genome,…
Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is…
Summary: Longer sequencing reads, with at least 200 bases per template are now common. While traditional aligners have adopted new strategies to improve the mapping of longer reads, aligners specific to bisulfite-sequencing were optimized…
Comprehensive discovery of structural variation (SV) in human genomes from DNA sequencing requires the integration of multiple alignment signals including read-pair, split-read and read-depth. However, owing to inherent technical…
Whole and targeted sequencing of human genomes is a promising, increasingly feasible tool for discovering genetic contributions to risk of complex diseases. A key step is calling an individual's genotype from the multiple aligned short read…
High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads…
RNA sequencing (RNA-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression and alternative splicing. Current RNA-seq protocols depend on high-throughput…
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently…