Results 21 to 30 of about 566,210 (290)
HMMploidy: inference of ploidy levels from short-read sequencing data [PDF]
Peer Community Journal, 2021 Abstract The inference of ploidy levels from genomic data is important to understand molecular mechanisms underpinning genome evolution. However, current methods based on allele frequency and sequencing depth variation do not have power to infer ploidy levels at low-and mid-depth sequencing data, as they do not ...
Soraggi S +6 more
europepmc +4 more sources
Fast search of thousands of short-read sequencing experiments [PDF]
Nature Biotechnology, 2016 The amount of sequence information in public repositories is growing at a rapid rate. Although these data are likely to contain clinically important information that has not yet been uncovered, our ability to effectively mine these repositories is limited.
Solomon, Brad, Kingsford, Carl
openaire +2 more sources
Software for pre-processing Illumina next-generation sequencing short read sequences [PDF]
Source Code for Biology and Medicine, 2014 When compared to Sanger sequencing technology, next-generation sequencing (NGS) technologies are hindered by shorter sequence read length, higher base-call error rate, non-uniform coverage, and platform-specific sequencing artifacts. These characteristics lower the quality of their downstream analyses, e.g.
Chen, Chuming +3 more
openaire +2 more sources
ABySS: A parallel assembler for short read sequence data [PDF]
Genome Research, 2009 Widespread adoption of massively parallel deoxyribonucleic acid (DNA) sequencing instruments has prompted the recent development of de novo short read assembly algorithms. A common shortcoming of the available tools is their inability to efficiently assemble vast amounts of data generated from large-scale sequencing projects, such as the sequencing of ...
Jared T, Simpson +5 more
openaire +2 more sources
A sensitive short read homology search tool for paired-end read sequencing data
BMC Bioinformatics, 2017 Background Homology search is still a significant step in functional analysis for genomic data. Profile Hidden Markov Model-based homology search has been widely used in protein domain analysis in many different species.
Prapaporn Techa-Angkoon +2 more
doaj +1 more source
Compression of short-read sequences using path encoding [PDF]
Bioinformatics, 2014 AbstractStoring, transmitting, and archiving the amount of data produced by next generation sequencing is becoming a significant computational burden. For example, large-scale RNA-seq meta-analyses may now routinely process tens of terabytes of sequence.
Kingsford, Carl, Patro, Rob
openaire +3 more sources
Base calling for high-throughput short-read sequencing: dynamic programming solutions [PDF]
, 2013 Shreepriya Das and Haris Vikalo are with the Electrical and Computer Engineering Department, The University of Texas at Austin, Austin, Texas 78712, USABackground: Next-generation DNA sequencing platforms are capable of generating millions of reads in ...
Das, Shreepriya, Vikalo, Haris
core +3 more sources
Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing. [PDF]
, 2020 Recent efforts to comprehensively characterize great ape genetic diversity using short-read sequencing and single-nucleotide variants have led to important discoveries related to selection within species, demographic history, and lineage-specific traits.
Andrés, Aida M +7 more
core +3 more sources
Discovery and genotyping of structural variation from long-read haploid genome sequence data [PDF]
, 2016 In an effort to more fully understand the full spectrum of human genetic variation, we generated deep single-molecule, real-time (SMRT) sequencing data from two haploid human genomes.
Boitano, Matthew +15 more
core +2 more sources
An analysis of the feasibility of short read sequencing [PDF]
Nucleic Acids Research, 2005 Several methods for ultra high-throughput DNA sequencing are currently under investigation. Many of these methods yield very short blocks of sequence information (reads). Here we report on an analysis showing the level of genome sequencing possible as a function of read length.
Whiteford, N. +7 more
openaire +6 more sources