Sentences with phrase «short read sequences»

Modern DNA sequencing technologies predominantly produce short read sequences.

«As medical researchers, if we depend only on short read sequences, there's a chink in our armor.

Short read sequencing has allowed exact identification and calling of single nucleotide polymorphisms and short indels and has substantially advanced the study of human populations.

Current research projects include sequencing the wheat genome through a combination of Illumina short read sequencing and long sequence reads using the new Pacific Biosciences sequencers.

Genome assemblies obtained from short read sequencing technologies are often fragmented into many contigs because of the abundance of repetitive sequences.

Not exact matches

But short reads can be hard to interpret during the overlaying process and there hasn't been a way to sequence long fragments of DNA in a targeted and more efficient way.

One sequencing technology used by the researchers produces massive amounts of very short reads — about 150 to 250 bases in length.

The Y chromosome, like all DNA, is composed of a series of molecules called «bases» that are represented by the letters A, T, C, and G. Current genetic sequencing technologies produce «reads» of sequence that are much shorter than the entire length of the chromosome.

To their surprise and dismay, the genome turned out to contain long stretches of noncoding and repetitive DNA, which made it difficult to piece together the short reads produced by the sequencing machine.

To overcome the extreme genomic complexity, the team used new long - read sequencing technology that boosted the quality of the genome sequence obtained by more than one hundred fold over standard short - read approaches.

Modern genome sequencing methods make it relatively easy to read the individual «letters» in DNA, but only in short fragments.

Hanna applied new sequencing strategies to read millions of short genetic regions and used powerful computers and assembly software to compile the genome again.

Massively parallel sequencing technologies, while increasing the speed, improving the accuracy, and reducing the cost of genome sequencing, typically produce only short stretches of sequences called «reads» After sequencing, the reads are pieced back together with genome assembly software.

The work on gorilla and other human genomes clearly demonstrates that large swathes of genetic variation can't be understood with the short sequence - read approaches.

Two papers by Langmead and team, Ultrafast and memory - efficient alignment of short DNA sequences to the human genome and Fast gapped - read alignment with Bowtie 2, have been cited in more than 12,000 scientific studies since 2009.

The short size of the locus was ideal for 454 sequencing, and because single - molecule reads are generated, the authors were able to identify haplotypes of somatic hypermutations carried by individual leukemic cells.

We refer interested readers to systematic comparisons of other aspects of the next - generation sequencing pipeline, for example comparisons of benchtop high - throughput sequencing technologies [56], short - read mappers [57], variant callers [58] and variant - calling pipelines as a whole [59, 60].

REPdenovo: Inferring De Novo Repeat Motifs from Short Sequence Reads.

Our method, based ideally on 20x and 50x of NaS and Illumina reads respectively, provides an efficient and cost - effective way of sequencing microbial or small eukaryotic genomes in a very short time even in small facilities.

An open source computer program for ordering short DNA sequence reads into long DNA fragments with the aid of the barcodes is also provided.

We designed PhylOTU, the first computational tool for estimating the taxonomic composition of metagenomic samples from short, next - generation sequencing reads.

The recently launched Gemcode system adds a new dimension to short - read DNA sequencing, by enabling the ordering of millions of barcoded short sequence reads of 150 base pairs into long continuous DNA molecules of hundreds of thousands of base pairs in size.

«In our research project on pediatric leukemia we plan to use Gemcode to define the exact chromosomal breakpoints of large scale chromosomal rearrangements and repetitive sequences that are typical for leukemic cells, but are difficult to characterize in short sequence reads,» said Professor Ann - Christine Syvänen, who leads the Molecular Medicine group.

Short DNA fragments are not able to reassemble repetitive elements in the genome — for these hard to assemble regions longer sequence read information is needed.

Solved the problem of clustering short metegnomic sequencing reads into taxonomic groups by leveraging sequenced genomes and phylogenetic triangulation.

Although SV detection by short - read sequencing is by no means a solved problem, this class of variation is missed entirely by a SNP chip design.

The method enables use of widely available short - read DNA sequencing platforms to study long single molecules within a complex sample, without losing information of physical connection between sequencing reads from each molecule of origin.

However, since STRs are (by definition) short tandem repeats and massively parallel sequencing reads were initially very short, reconstructing STRs from WGS data wasn't really feasible.

The capabilities of next - gen sequencing would continue to surprise us: the Trace Archive couldn't hold them, and even the Short Read Archive ultimately failed.

One of SciLifeLab's research groups is the first site in Europe to obtain the new Gemcode system for phasing short - read DNA sequencing data.

Yet those who produce next - gen sequencing data are rapidly adopting this universal short read data format as the de facto standard.

During the pilot phase, the Project is analysing Illumina short - read sequence data on 2,512 samples from multiple locations in Africa and Asia, together with laboratory samples for benchmarking and methods development.

In 2012, Plessy et al. reported the expression of 955 OR genes using nanoCAGE, a methodology that captures the 5 ′ end of transcripts and generates short sequence reads around that region [29].

I'll be attending the coveted Marco Island meeting early next month (February 4 - 8), where I'll present a poster on my evaluations of short read aligners for next - gen sequencing data.

First, to distinguish between true variants and false positives in shorter, more error - prone sequencing reads.

Although such technologies are capable of generating vast amounts of sequencing data, the short read length makes it more difficult to assign how individual reads relate to each other.

Following the development of a computational pipeline, including a new de novo assembler for RNA virus genomes, to generate larger contiguous sequences (contigs) from the abundance of short sequence reads that characterise the data, another area that determines genome sequencing success is the quality and quantity of the input RNA.

Despite improvements in genomics technology, the detection of structural variants (SVs) from short - read sequencing still poses challenges, particularly for complex variation.

Despite advances in sequencing, structural variants (SVs) remain difficult to reliably detect due to the short read length (< 300bp) of 2nd generation sequencing.

Compared with short reads, the assemblies obtained from long - read sequencing platforms have much higher contig continuity and genome completeness as long fragments are able to extend paths into problematic or repetitive regions.

Short - read, high - throughput sequencing technology can not identify the chromosomal position of repetitive insertion sequences that typically flank horizontally acquired genes such as bacterial virulence genes and antibiotic resistance genes.

Small subunit (SSU) rRNA gene sequencing on second generation platforms leverages their deep sequencing and multiplexing capacity, but is limited in genetic resolution due to short read lengths.

Short - read sequencing works by splitting the DNA of various microscopic organisms into small pieces that can then be sequenced.

Long - read sequencing technologies were launched a few years ago, and in contrast with short - read sequencing technologies, they offered a promise of solving assembly problems for large and complex genomes.

Current genome assemblies are based on short - read sequencing data scaffolded based on homology to strain S288C.

Their complexity has been challenging to reconstruct from short - read sequencing data.

All short - read sequencing data have been deposited at the European Genome - phenome Archive (EGA, http://www.ebi.ac.uk/ega/), which is hosted by the EBI, under accession number EGAS00001000274.

Current massively parallel DNA sequencing technologies produce short sequence reads that are often unable to resolve haplotype information.

To address the issue of short sequencing reads, the Experimental Genomics group at SciLifeLab Stockholm, led by associate professor Afshin Ahmadian and his PhD students Erik Borgström and David Redin, has developed a new technique that is capable of analyzing millions of single DNA molecules in parallel, while maintaining information of how the genetic variants within these molecules are linked.

Completion of eukaryal genomes can be difficult task with the highly repetitive sequences along the chromosomes and short read lengths of second - generation sequencing.