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Long-read sequencing

Tìm thấy 15+ kết quả cho từ khóa "Long-read sequencing"

Completion of draft bacterial genomes by long-read sequencing of synthetic genomic pools

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Completion of draft bacterial genomes by long-read sequencing of synthetic genomic pools. Alternatively, hybrid assembly using both Illumina short reads and long reads generated by single molecule sequencing technologies can enable assembly of complete bacterial genomes, yet the high per-genome cost of long-read sequencing limits the widespread use of this approach in bacterial genomics.

Complete nontuberculous mycobacteria whole genomes using an optimized DNA extraction protocol for long-read sequencing

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Mycobacterial DNA extraction for whole-genome sequencing from early positive liquid (MGIT) cultures. Ultra-long read sequencing protocol for RAD004, on protocols.Io.. Assembly of the mycobacterial Cell Wall. scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. visualizing and processing long-read sequencing data

PacBio single-molecule long-read sequencing shed new light on the complexity of the Carex breviculmis transcriptome

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PacBio single-molecule long-read sequencing shed new light on the complexity of the Carex breviculmis transcriptome. However, the current transcriptome is not satisfactory mainly because of the enormous difficulty in obtaining full-length transcripts..

PacBio single molecule long-read sequencing provides insight into the complexity and diversity of the Pinctada fucata martensii transcriptome

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Characterization and analysis of the transcriptome in Gymnocypris selincuoensis on the Qinghai-Tibetan plateau using single-molecule long-read sequencing and RNA-seq. Characterization of the human ESC transcriptome by hybrid sequencing.. Li QS, Li Y, Song JY, Xu HB, Xu J, Zhu YJ, et al. H+-coupled nutrient, micronutrient and drug transporters in the mammalian small intestine.

Re-examination of two diatom reference genomes using long-read sequencing

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Long-read sequencing has the potential to give rise to highly contiguous scaffolds representing all or most of an organism’s chromosomes (see e.g., the recent Nanopore sequencing of the model nematode C. We view our long-read assemblies as additional genomic datasets that do not replace but complement and enhance the existing Sanger-based reference genomes – in isolation, neither provides a complete picture of the P.

A new method for long-read sequencing of animal mitochondrial genomes: Application to the identification of equine mitochondrial DNA variants

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In conclusion, the read coverage of the mitochondrial genome was complete and unbiased in our tested conditions.. Long-read distribution and coverage of the mitochondrial genome. Since we obtained a good coverage of the mitochondrial genome, we wondered about the proportion of long- reads covering a significant portion of the mitochondrial DNA.

Yes, we can use it: A formal test on the accuracy of low-pass nanopore long-read sequencing for mitophylogenomics and barcoding research using the Caribbean spiny lobster Panulirus argus

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Barcoding using long-read mitochondrial genome assemblies.

Temporal salt stress-induced transcriptome alterations and regulatory mechanisms revealed by PacBio long-reads RNA sequencing in Gossypium hirsutum

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Biochemical response to salt stress (400 mM) was measured at 0 h, 3 h, 12 h, 24 h and 48 h post stress intervals and single- molecule long-read sequencing technology from Pacific Biosciences (PacBio) combined with the unique molecular identifiers approach was used to identify differentially expressed genes (DEG).. Prolonged salt stress duration induces high number of DEGs.. response to salt stress.

Transcriptome analysis and molecular mechanism of linseed (Linum usitatissimum L.) drought tolerance under repeated drought using single-molecule long-read sequencing

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Therefore, we reveal the molecular mechanism difference between Z141 and NY-17 in response to drought stress using single-molecule long-read tran- scriptome sequencing..

The complete chloroplast genome of greater duckweed (Spirodela polyrhiza 7498) using PacBio long reads: Insights into the chloroplast evolution and transcription regulation

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In 2008, the first duckweed chloroplast genome (L.minor) was sequenced by Sanger sequencing [11]. In the meanwhile, the duckweed nuclear genomes have become more complete with the expan- sion of sequencing technology. Long-read sequencing, such as SMRT (Single Molecule Real-Time) technology emerged in 2009 [17] has been widely applied in sequen- cing the chloroplast genomes with the improved con- tiguity and accuracy.

Capture of complete ciliate chromosomes in single sequencing reads reveals widespread chromosome isoforms

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Overall, hybrid error correction outperforms long-read-only error correction at all sequencing depths (Fig. 5), and while the number of contigs recovered by hybrid error correction begins to saturate with eight flow cells’ worth of data, the steep slope of the long-read-only curve suggests that considerably more sequencing depth would be necessary to correct all chromosomes using only long reads.. 4 Long-read sequencing reveals underlying structural variation among chromosomes.

Genome re-sequencing and reannotation of the Escherichia coli ER2566 strain and transcriptome sequencing under overexpression conditions

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Various de novo assembly softwares were used to construct a confident and long bp) scaffold, and assembly results for each step were assessed by alignment of final sequences back to the reference genome (Fig. The technical difference between short-read sequencing and single mol- ecule long-read sequencing may result in the generation of inverted region. coli ER2566 strain in our lab did not cause mutation in the genomic sequence..

Comparison of multiple algorithms to reliably detect structural variants in pears

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Of the two software packages using long-read sequencing data, SVIM showed higher sensitivity, probably because SVIM collects, clusters and combines SV signatures from read alignments [32]. selected five software packages for finding overlapping SVs, and finally validated the accuracy of the overlapping SVs.. In our study, we found that the depth of NGS and long read sequencing absolutely affected the number of SVs called (Fig.

Third-generation sequencing and metabolome analysis reveal candidate genes and metabolites with altered levels in albino jackfruit seedlings

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Characterization and analysis of the transcriptome in Opisina arenosella from different developmental stages using single-molecule real-time transcript sequencing and RNA-sEq. A global survey of the transcriptome of allopolyploid Brassica napus based on single-molecule long-read isoform sequencing and Illumina-based RNA sequencing data. The developmental dynamics of the Populus stem transcriptome. Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing

Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

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A further reduction of the relatively high error rate of long-reads, or the use of more accurate long-read sequencing technolo- gies, could simplify the generation of haplotype-level gen- ome assemblies in the future by reducing noise [70]..

Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma)

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Long-read sequence assembly of the gorilla genome. https://doi.org/10.1126/science.aae0344.. https://doi.org/10.1038/ng.3802.. https://doi.org/10.1186/s . https://doi.org/10.1093/. https://doi.org/10.1038/nature25458.. doi.org/10.1038/s . https://doi.org/10.1093/bioinformatics/btp352.. https://doi.. org/10.1093/bioinformatics/btm071.. https://doi.org/10.1038/nature12111.. https://doi.org/10.1038/nature05846.. https://doi.org/10.1038/nature10944.. https://doi.org/10.1038/nature10342.. org/10.1073/

Consistent ultra-long DNA sequencing with automated slow pipetting

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By automating the slow pipetting of library preparation reagents, SNAILS increases the consistency and throughput of long read Nanopore sequencing.. Keywords: Oxford Nanopore technologies, GridION, MinION, DNA sequencing, Long read sequencing, Ultra-long, Ultra-high molecular weight DNA, de novo assembly. Illumina reads aligned to GRCh38 better than other long read sequencing technologies [4].

Using short read sequencing to characterise balanced reciprocal translocations in pigs

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Therefore the aim of this study was to test the possibilities of paired end short read sequencing for detection of balanced RTs at different sequencing coverage depth and investigate the breakpoints and junctions of the translocations using the sequence information.. The Giemsa stained pictures of the karyo- type of the carriers are in Figs.

Illuminating the dark side of the human transcriptome with long read transcript sequencing

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To gain a better understanding of the effect that RNA degradation may have on long read based annotations, we analyzed the transcript models which had matching 3′ exon-intron structure between the TAMA High (135, 218 transcripts), Polish (126,288 transcripts), and Ensembl v transcripts) annotations to see which annotation had longer 5′ representation (Table 2)..

Hecaton: Reliably detecting copy number variation in plant genomes using short read sequencing data

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As a large fraction of calls could not be validated using long read data, due to the highly repeti- tive nature of the Mo17 assembly (Additional File 2: Table S3), we only report performance metrics for calls that overlap for at least 50% of their length with genes or the 5000 bp interval upstream or downstream of genes.