19,439 research outputs found
BigWig and BigBed: enabling browsing of large distributed datasets
Summary: BigWig and BigBed files are compressed binary indexed files containing data at several resolutions that allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser. The visualization is implemented using a multi-layered software approach that takes advantage of specific capabilities of web-based protocols and Linux and UNIX operating systems files, R trees and various indexing and compression tricks. As a result, only the data needed to support the current browser view is transmitted rather than the entire file, enabling fast remote access to large distributed data sets
A resource-frugal probabilistic dictionary and applications in (meta)genomics
Genomic and metagenomic fields, generating huge sets of short genomic
sequences, brought their own share of high performance problems. To extract
relevant pieces of information from the huge data sets generated by current
sequencing techniques, one must rely on extremely scalable methods and
solutions. Indexing billions of objects is a task considered too expensive
while being a fundamental need in this field. In this paper we propose a
straightforward indexing structure that scales to billions of element and we
propose two direct applications in genomics and metagenomics. We show that our
proposal solves problem instances for which no other known solution scales-up.
We believe that many tools and applications could benefit from either the
fundamental data structure we provide or from the applications developed from
this structure.Comment: Submitted to PSC 201
De Novo Assembly of Nucleotide Sequences in a Compressed Feature Space
Sequencing technologies allow for an in-depth analysis
of biological species but the size of the generated datasets
introduce a number of analytical challenges. Recently, we
demonstrated the application of numerical sequence representations
and data transformations for the alignment of short
reads to a reference genome. Here, we expand out approach
for de novo assembly of short reads. Our results demonstrate
that highly compressed data can encapsulate the signal suffi-
ciently to accurately assemble reads to big contigs or complete
genomes
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novoBreak: local assembly for breakpoint detection in cancer genomes.
We present novoBreak, a genome-wide local assembly algorithm that discovers somatic and germline structural variation breakpoints in whole-genome sequencing data. novoBreak consistently outperformed existing algorithms on real cancer genome data and on synthetic tumors in the ICGC-TCGA DREAM 8.5 Somatic Mutation Calling Challenge primarily because it more effectively utilized reads spanning breakpoints. novoBreak also demonstrated great sensitivity in identifying short insertions and deletions
A comprehensive evaluation of alignment algorithms in the context of RNA-seq.
Transcriptome sequencing (RNA-Seq) overcomes limitations of previously used RNA quantification methods and provides one experimental framework for both high-throughput characterization and quantification of transcripts at the nucleotide level. The first step and a major challenge in the analysis of such experiments is the mapping of sequencing reads to a transcriptomic origin including the identification of splicing events. In recent years, a large number of such mapping algorithms have been developed, all of which have in common that they require algorithms for aligning a vast number of reads to genomic or transcriptomic sequences. Although the FM-index based aligner Bowtie has become a de facto standard within mapping pipelines, a much larger number of possible alignment algorithms have been developed also including other variants of FM-index based aligners. Accordingly, developers and users of RNA-seq mapping pipelines have the choice among a large number of available alignment algorithms. To provide guidance in the choice of alignment algorithms for these purposes, we evaluated the performance of 14 widely used alignment programs from three different algorithmic classes: algorithms using either hashing of the reference transcriptome, hashing of reads, or a compressed FM-index representation of the genome. Here, special emphasis was placed on both precision and recall and the performance for different read lengths and numbers of mismatches and indels in a read. Our results clearly showed the significant reduction in memory footprint and runtime provided by FM-index based aligners at a precision and recall comparable to the best hash table based aligners. Furthermore, the recently developed Bowtie 2 alignment algorithm shows a remarkable tolerance to both sequencing errors and indels, thus, essentially making hash-based aligners obsolete
SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner
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 computational power of both CPU and GPU with optimized algorithms, delivers
high speed and sensitivity simultaneously. Compared with widely adopted
aligners including BWA, Bowtie2, SeqAlto, GEM and GPU-based aligners including
BarraCUDA and CUSHAW, SOAP3-dp is two to tens of times faster, while
maintaining the highest sensitivity and lowest false discovery rate (FDR) on
Illumina reads with different lengths. Transcending its predecessor SOAP3,
which does not allow gapped alignment, SOAP3-dp by default tolerates alignment
similarity as low as 60 percent. Real data evaluation using human genome
demonstrates SOAP3-dp's power to enable more authentic variants and longer
Indels to be discovered. Fosmid sequencing shows a 9.1 percent FDR on newly
discovered deletions. SOAP3-dp natively supports BAM file format and provides a
scoring scheme same as BWA, which enables it to be integrated into existing
analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and
Tianhe-1A.Comment: 21 pages, 6 figures, submitted to PLoS ONE, additional files
available at "https://www.dropbox.com/sh/bhclhxpoiubh371/O5CO_CkXQE".
Comments most welcom
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A novel NGS library preparation method to characterize native termini of fragmented DNA.
Biological and chemical DNA fragmentation generates DNA molecules with a variety of termini, including blunt ends and single-stranded overhangs. We have developed a Next Generation Sequencing (NGS) assay, XACTLY, to interrogate the termini of fragmented DNA, information traditionally lost in standard NGS library preparation methods. Here we describe the XACTLY method, showcase its sensitivity and specificity, and demonstrate its utility in in vitro experiments. The XACTLY assay is able to report relative abundances of all lengths and types (5' and 3') of single-stranded overhangs, if present, on each DNA fragment with an overall accuracy between 80-90%. In addition, XACTLY retains the sequence of each native DNA molecule after fragmentation and can capture the genomic landscape of cleavage events at single nucleotide resolution. The XACTLY assay can be applied as a novel research and discovery tool for fragmentation analyses and in cell-free DNA
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