Sentences with phrase «sequencing reading»

The famous sequence reads:

Stool samples were dominated by Bacteroides and Bifidobacterium comprising half of sequence reads, with Streptococcus, Clostridium, Enterococcus, Blautia, Veillonella, Lactobacillus, Staphylococcus, Planococcus, and others representing the remainder (Table 2).

Grechkin and his team tested their tool on two popular data repositories maintained by the NCBI — GEO and the Sequence Read Archive (SRA).

Uniform alignments of sequence reads, corresponding to on - target and off - target in vitro cleavage sites, were computationally identified.

Sequencing nuclear genomes requires sequencing the DNA library many times over, increasing the «depth» of sequence reads at each base.

In light of these findings and since tRNAs are repeat sequences themselves, the team had to devise a complex and stringent scheme with which they mapped the deep sequencing reads.

The key to their success was to generate long sequencing reads, producing an assembly with not many more scaffolds than C. krusei has chromosomes.

High - throughput sequencing of the library and alignment of sequencing reads to a reference genome identifies the profile of rNMP incorporation events.

A new sequencing technology based on longer sequence reads allows missing genes and missing forms of genetic variation to be discovered for the first time.

The researchers used Single Molecule, Real - Time (SMRT) sequencing technology, the assembly tools Falcon and QUIVER, and other techniques to generate long sequence reads.

The poor apparent coverage was the result of high sequence divergence of the TMAdV genome from SAdV - 18, which hindered the identification of most of the 16,524 actual deep sequencing reads derived from TMAdV (Fig. 2B, red).

Sequencing data are available from the NCBI sequence read archive (SRA) database under accession numbers SRS1407451 (CTC) and SRS1407453 (HXH), and mitochondrial genomes are available in GenBank under accessions KX379528 and KX379529, respectively.

To explore the kinetics of gene selection in vivo, we plotted the percentage of sequencing reads mapped to genes in the Bt genome over time and examined genes constituting > 0.2 % of total reads.

Raw sequence data are deposited in the Sequence Read Archive (BioSample accession SAMN02358582 - SAMN02358599).

Six strains were assembled from pair - end Illumina sequence reads against TAIR10 by the Joint Genome Institute.

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

Frequency distribution of 17 - mer sequencing reads in the Argopecten irradians draft genome, as a function of sequencing depth.

Sequences were acquired for both an even mixture of the ten plasmids, and a staggered mixture (a total of 28,161 sequence reads; Additional File 4).

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

Alignment of sequencing reads to the reference sequence using proprietary GEM alignment pipeline

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.

To meet the challenge they used «next - generation» sequencing techniques, in which the DNA is broken up randomly into numerous small segments and assembled into longer sequence reads by identifying the overlapping ends.

«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.

ViraPipe: Scalable Parallel Pipeline for Viral Metagenome Analysis from Next Generation Sequencing Reads

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.

Szabó and colleagues required a minimum of 10 sequence reads to call a gene as imprinted.

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

MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads — Thomas Petersen — May 2017

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.

MRD testing simply requires additional cell equivalents of DNA to be sampled and a higher sequencing read depth.

We mapped sequencing reads to the Nvit1.0 assembly [15] using a TopHat2 [45] and Stampy [46], and then mapped reads which failed to align to the genome against the OGSv2 predicted transcriptome with bowtie2 [47] to improve mapping sensitivity (see methods for details).

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.

We used a combination of TopHat2 [45] and Stampy [46] to map our sequencing reads to the reference scaffolds, in order to leverage the unique strengths of each program and maximize mapping success.

In most samples, the first three contributed the majority of the sequence reads.

The data include sequence reads, their mappings to a reference human genome, and variations detected against the reference human genome.

The data were submitted to the Sequence Reads Archive (SRA) of NCBI (accession number: SRP021071).

After sequence read quality and damage filtering (Supplementary Fig. 4), we called per - individual consensus sequences for nucleotide positions covered by a minimum of two independent reads.

We therefore used Cufflinks to generate de novo assemblies from the sequencing reads in order to identify full length transcripts for OR and VR genes [30].

ChIP - Seq sequencing reads were mapped to the human genome (GRCh37 / hg19) using Bowtie2 with default parameters (v2.1.0, [27]-RRB-.

Using STAR 2.3 [47], sequencing reads were aligned to the GRCm38 mouse reference genome, annotation version 68 of the Ensembl mouse genome database (http://jul2012.archive.ensembl.org/info/data/ftp/index.html).

Michael Schatz is a computational biologist and an expert at large - scale computational examination of DNA sequencing data, including the alignment, assembly, and analysis of next - generation sequencing reads.

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].

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

Below are the sequencing reads in grey, and blue lines join reads that span exon junctions.

Forward and reverse sequence reads were trimmed of adapter sequences and overlapping reads were merged41, enforcing a minimum 11 - nt overlap and base quality score of 20.

From a total of 10,896,742 raw deep sequencing reads, 40,844 reads were mapped to the 22Rv1 - associated XMRV genome (Fig. 5, «LNCaP (from 2003)»), and the resulting consensus assembly was found to be identical to 22Rv1 - associated XMRV (Fig. 6, «LNCaP (from 2003, consensus)»).

The long sequencing reads produced by Oxford Nanopore's platforms enable the assembly of genomes with superior contiguity compared to those produced by second generation technologies.

SNP analysis of deep sequencing reads corresponding to the XMRV genomes of 22Rv1 (A) and LNCaP (B), as well as the mitochondrial genomes of these two cell lines (C) was performed.

All sequence reads were aligned to (1) plasmid sequences available in the NCBI RefSeq database (2138 sequences) and (2) sequences in GenBank nucleotide database annotated as plasmids (\ organism feature = «plasmid»)(9815 sequences).