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Illumina sequencing data
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Gene annotations, such as those in GENCODE, are derived primarily from alignments of spliced cDNA sequences and protein sequences. The impact of RNA-seq data on annotation has been confined to major projects like ENCODE and Illumina Body Map 2.0.
14p
vialfrednobel
29-01-2022
10
0
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Mash extends the MinHash dimensionality-reduction technique to include a pairwise mutation distance and P value significance test, enabling the efficient clustering and search of massive sequence collections. Mash reduces large sequences and sequence sets to small, representative sketches, from which global mutation distances can be rapidly estimated.
14p
viaristotle
29-01-2022
7
0
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In high-throughput sequencing data, performance comparisons between computational tools are essential for making informed decisions at each step of a project. Simulations are a critical part of method comparisons, but for standard Illumina sequencing of genomic DNA, they are often oversimplified, which leads to optimistic results for most tools.
37p
viarchimedes
26-01-2022
7
1
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In the present study, microalgal biomass (Anabeana circinalis and Scenedesmus quadricauda) was used as biofertilizer in cucumber cultivation. The response of cucumber growth characters to microalgal biofertilizer was evaluated. Moreover, rhizosphere microbial diversity and community composition of cucumber was analyzed through 16S rRNA high-throughput Illumina sequencing data. The results showed that microalgal biomass as biofertilizer significantly promoted height, number of leaves and flower buds, and stem diameter of cucumber. The application of a high concentration of S.
12p
tudichquannguyet
29-11-2021
5
2
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Gibberellins (GAs) can have profound effects on growth and development in higher plants. In contrast to their flowering-promotive role in many well-studied plants, GAs can repress flowering in woody perennial plants such as apple (Malus x domestica Borkh.).
15p
visilicon2711
20-08-2021
7
1
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Our understanding of the pig transcriptome is limited. RNA transcript diversity among nine tissues was assessed using poly(A) selected single-molecule long-read isoform sequencing (Iso-seq) and Illumina RNA sequencing (RNA-seq) from a single White cross-bred pig.
19p
visilicon2711
20-08-2021
8
1
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Mitochondrial genomic sequences are known to be variable. Comparative analyses of mitochondrial genomes can reveal the nature and extent of their variation. Results: Draft mitochondrial genomes of 16 Tremella fuciformis isolates (TF01-TF16) were assembled from Illumina and PacBio sequencing data.
12p
vijeeni2711
24-07-2021
8
0
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In the past decades, next generation sequencing has improved our understanding of bacterial diversity in soil (Simon and Daniel, 2011). Nguyen et al. (2016) used 454 pyrosequencing to detect bacterial community in Korean ginseng cultivated soil in Korea. But the high cost of 454 pyrosequencing tools have limited small laboratories‟ access. Due to that, in 2001 Illumina developed MiSeq which have enabled deep sequencing of microbial communities at a lower cost (Caporaso et al., 2012).
9p
nguathienthan11
06-04-2021
14
2
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Deep-sequencing allows for an in-depth characterization of sequence variation in complex populations. However, technology associated errors may impede a powerful assessment of low-frequency mutations. Fortunately, base calls are complemented with quality scores which are derived from a quadruplet of intensities, one channel for each nucleotide type for Illumina sequencing.
11p
vikentucky2711
26-11-2020
11
1
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DNBSEQ™ platforms are new massively parallel sequencing (MPS) platforms that use DNA nanoball technology. Use of data generated from DNBSEQ™ platforms to detect single nucleotide variants (SNVs) and small insertions and deletions (indels) has proven to be quite effective, while the feasibility of copy number variants (CNVs) detection is unclear.
14p
vikentucky2711
24-11-2020
14
1
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Illumina is the most widely used next generation sequencing technology and produces millions of short reads that contain errors. These sequencing errors constitute a major problem in applications such as de novo genome assembly, metagenomics analysis and single nucleotide polymorphism discovery.
7p
vioklahoma2711
19-11-2020
22
1
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Illumina’s sequencing platforms are currently the most utilised sequencing systems worldwide. The technology has rapidly evolved over recent years and provides high throughput at low costs with increasing read-lengths and true paired-end reads.
15p
vioklahoma2711
19-11-2020
18
1
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Recently, rapid improvements in technology and decrease in sequencing costs have made RNA-Seq a widely used technique to quantify gene expression levels. Various normalization approaches have been proposed, owing to the importance of normalization in the analysis of RNA-Seq data.
9p
vioklahoma2711
19-11-2020
5
0
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Recently, many standalone applications have been proposed to correct sequencing errors in Illumina data. The key idea is that downstream analysis tools such as de novo genome assemblers benefit from a reduced error rate in the input data.
13p
viflorida2711
30-10-2020
7
2
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Aligning short reads to a reference genome is an important task in many genome analysis pipelines. This task is computationally more complex when the reference genome is provided in the form of a de Bruijn graph instead of a linear sequence string.
10p
viconnecticut2711
28-10-2020
15
1
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Several standalone error correction tools have been proposed to correct sequencing errors in Illumina data in order to facilitate de novo genome assembly. However, in a recent survey, we showed that state-of-the-art assemblers often did not benefit from this pre-correction step.
13p
vijisoo2711
27-10-2020
15
1
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To increase the accuracy of microbiome data analysis, solving the technical limitations of the existing sequencing machines is required. Quality trimming is suggested to reduce the effect of the progressive decrease in sequencing quality with the increased length of the sequenced library.
10p
vicolorado2711
23-10-2020
16
1
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The European Community has adopted very restrictive policies regarding the dissemination and use of genetically modified organisms (GMOs). In fact, a maximum threshold of 0.9% of contaminating GMOs is tolerated for a “GMOfree” label.
17p
vicolorado2711
22-10-2020
19
1
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MicroRNAs play important roles in the adaptive responses of plants to nutrient deficiencies. Most research, however, has focused on nitrogen (N), phosphorus (P), sulfur (S), copper (Cu) and iron (Fe) deficiencies, limited data are available on the differential expression of miRNAs and their target genes in response to deficiencies of other nutrient elements.
15p
vihashirama2711
21-05-2020
17
1
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Coscinium fenestratum (Gaertn.) Colebr, a important medicinal vine is considered as critically endangered or restricted to the humus rich soil. It has abundant use in ayurvedic, siddha, tibetan medicine system. The plant is already Red listed and at the verge of extinction. So a transcriptome study and the GC analysis of the plant are vital. The research provides information on its transcriptome and its stability which can be used for further studies. The leaf tissue of C.fenestratum was collected, sequenced using illumina paired end sequencing.
5p
cothumenhmong1
10-12-2019
23
0
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