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Long read mapping
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High sequence identity between segmental duplications (SDs) can facilitate copy number variants (CNVs) via non-allelic homologous recombination (NAHR). These CNVs are one of the fundamental causes of genomic disorders such as the 3q29 deletion syndrome (del3q29S).
17p
vicwell
29-02-2024
2
1
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Long-read sequencing enables variant detection in genomic regions that are considered difficult-to-map by short-read sequencing. To fully exploit the benefits of longer reads, here we present a deep learning method NanoCaller, which detects SNPs using long-range haplotype information, then phases long reads with called SNPs and calls indels with local realignment.
33p
viarchimedes
26-01-2022
8
0
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Creating gapless telomere-to-telomere assemblies of complex genomes is one of the ultimate challenges in genomics. We use two independent assemblies and an optical map-based merging pipeline to produce a maize genome (B73-Ab10) composed of 63 contigs and a contig N50 of 162 Mb. T
17p
viarchimedes
26-01-2022
7
0
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Next-generation sequencing requires sufficient DNA to be available. If limited, whole-genome amplification is applied to generate additional amounts of DNA. Such amplification often results in many chimeric DNA fragments, in particular artificial palindromic sequences, which limit the usefulness of long sequencing reads.
12p
vitzuyu2711
29-09-2021
10
1
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The lower Dipteran fungus fly, Sciara coprophila, has many unique biological features that challenge the rule of genome DNA constancy. For example, Sciara undergoes paternal chromosome elimination and maternal X chromosome nondisjunction during spermatogenesis, paternal X elimination during embryogenesis, intrachromosomal DNA amplification of DNA puff loci during larval development, and germline-limited chromosome elimination from all somatic cells.
23p
vitzuyu2711
29-09-2021
12
1
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The plastid acquisition by secondary endosymbiosis is a driving force for the algal evolution, and the comparative genomics was required to examine the genomic change of symbiont. Therefore, we established a pipeline of a de novo assembly of middle-sized genomes at a low cost and with high quality using long and short reads.
12p
vitzuyu2711
29-09-2021
8
1
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The ability to generate long sequencing reads and access long-range linkage information is revolutionizing the quality and completeness of genome assemblies. Here we use a hybrid approach that combines data from four genome sequencing and mapping technologies to generate a new genome assembly of the honeybee Apis mellifera.
19p
visilicon2711
20-08-2021
10
1
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Promising prospects of nanopore sequencing for algal hologenomics and structural variation discovery
The MinION Access Program (MAP, 2014–2016) allowed selected users to test the prospects of long nanopore reads for diverse organisms and applications through the rapid development of improving chemistries.
17p
viansan2711
30-07-2021
11
1
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The marine diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum are valuable model organisms for exploring the evolution, diversity and ecology of this important algal group. Their reference genomes, published in 2004 and 2008, respectively, were the product of traditional Sanger sequencing.
25p
vilichoo2711
23-06-2021
12
1
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Whole genome sequencing is effective at identification of small variants, but because it is based on short reads, assessment of structural variants (SVs) is limited. The advent of Optical Genome Mapping (OGM), which utilizes long fluorescently labeled DNA molecules for de novo genome assembly and SV calling, has allowed for increased sensitivity and specificity in SV detection.
16p
vilichoo2711
25-06-2021
21
1
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The amount of non-unique sequence (non-singletons) in a genome directly affects the difficulty of read alignment to a reference assembly for high throughput-sequencing data. Although a longer read is more likely to be uniquely mapped to the reference genome, a quantitative analysis of the influence of read lengths on mappability has been lacking.
12p
viwyoming2711
16-12-2020
13
1
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As resequencing projects become more prevalent across a larger number of species, accurate variant identification will further elucidate the nature of genetic diversity and become increasingly relevant in genomic studies.
7p
vikentucky2711
26-11-2020
9
0
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Rapid evolutions in sequencing technology force read mappers into flexible adaptation to longer reads, changing error models, memory barriers and novel applications. Results: ALFALFA achieves a high performance in accurately mapping long single-end and paired-end reads to gigabase-scale reference genomes, while remaining competitive for mapping shorter reads.
11p
vikentucky2711
24-11-2020
11
1
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Scaffolding is an essential step in the genome assembly process. Current methods based on large fragment paired-end reads or long reads allow an increase in contiguity but often lack consistency in repetitive regions, resulting in fragmented assemblies.
9p
vioklahoma2711
19-11-2020
22
3
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The long-range sequencing information captured by linked reads, such as those available from 10× Genomics (10xG), helps resolve genome sequence repeats, and yields accurate and contiguous draft genome assemblies. We introduce ARKS, an alignment-free linked read genome scaffolding methodology that uses linked reads to organize genome assemblies further into contiguous drafts.
10p
viconnecticut2711
28-10-2020
9
1
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Haplotype assembly is the process of assigning the different alleles of the variants covered by mapped sequencing reads to the two haplotypes of the genome of a human individual. Long reads, which are nowadays cheaper to produce and more widely available than ever before, have been used to reduce the fragmentation of the assembled haplotypes since their ability to span several variants along the genome.
19p
viconnecticut2711
28-10-2020
17
1
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The long reads produced by third generation sequencing technologies have significantly boosted the results of genome assembly but still, genome-wide assemblies solely based on read data cannot be produced.
19p
vicolorado2711
22-10-2020
11
1
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In this talk, I will address the problem of grounding linguistic analysis in control applications, such as game playing and robot navigation. We assume access to natural language documents that describe the desired behavior of a control algorithm (e.g., game strategy guides). Our goal is to demonstrate that knowledge automatically extracted from such documents can dramatically improve performance of the target application. First, I will present a reinforcement learning algorithm for learning to map natural language instructions to executable actions. ...
1p
bunthai_1
06-05-2013
47
2
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Ever wonder why women can brush their teeth while walking and talking on various subjects while men generally find this very difficult to do? Why 99 percent of all patents are registered by men? Why stressed women talk? Why so many husbands hate shopping? According to Barbara and Allan Pease, science now confirms that "the way our brains are wired and the hormones pulsing through our bodies are the two factors that largely dictate, long before we are born, how we will think and behave. Our instincts are simply our genes determining how our bodies will behave in given sets...
305p
jojobn
08-11-2010
164
44
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