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Assembly pipeline
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Ebook "Computer organization and design: The hardware/software interface (3rd edition)" presents an entire MIPS instruction set—instruction by instruction—the fundamentals of assembly language, computer arithmetic, pipelining, memory hierarchies and I/O. A new aspect of the third edition is the explicit connection between program performance and CPU performance. The authors show how hardware and software components--such as the specific algorithm, programming language, compiler, ISA and processor implementation impact program performance.
689p
tichhythan
17-08-2023
10
6
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In this paper we present IntroMap, a bioinformatics pipeline for the screening of candidate plants through the application of signal processing techniques to NGS data, using alignment to a reference genome sequence (annotation is not required) that shares homology with the recurrent parental cultivar, and without the need for de novo assembly of the read data or variant calling.
12p
vinarcissa
21-03-2023
6
1
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The human reference genome is still incomplete, especially for those population-specific or individual-specific regions, which may have important functions. Here, we developed a HUman Pan-genome ANalysis (HUPAN) system to build the human pan-genome.
11p
vielonmusk
30-01-2022
10
0
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Sequencing technology and assembly algorithms have matured to the point that high-quality de novo assembly is possible for large, repetitive genomes. Current assemblies traverse transposable elements (TEs) and provide an opportunity for comprehensive annotation of TEs. Numerous methods exist for annotation of each class of TEs, but their relative performances have not been systematically compared.
18p
vielonmusk
30-01-2022
14
0
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Population-level comparisons of prokaryotic genomes must take into account the substantial differences in gene content resulting from horizontal gene transfer, gene duplication and gene loss.
21p
viarchimedes
26-01-2022
12
0
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Our assembly-free linkage analysis pipeline (AFLAP) identifies segregating markers as k-mers in the raw reads without using a reference genome assembly for calling variants and provides genotype tables for the construction of unbiased, high-density genetic maps without a genome assembly.
26p
viarchimedes
26-01-2022
16
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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Continuous developments in DNA sequencing technologies aim at alleviating the technical challenges that limit the ability to assemble sequence data into full-length chromosomes. Conventional assembly programs and pipelines often encounter difficulties to close gaps in draft genome assemblies introduced by regions enriched in repeated elements.
22p
viarchimedes
26-01-2022
14
0
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Microsatellite polymorphism has always been a challenge for genome assembly and sequence alignment due to sequencing errors, short read lengths, and high incidence of polymerase slippage in microsatellite regions. Despite the information they carry being very valuable, microsatellite variations have not gained enough attention to be a routine step in genome sequence analysis pipelines.
10p
thiencuuchu
27-11-2021
8
1
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Inferring phylogenetic trees for newly recovered genomes from metagenomic samples is very useful in determining the identities of uncultivated microorganisms. Even though 16S ribosomal RNA small subunit genes have been established as “gold standard” markers for inferring phylogenetic trees, they usually cannot be assembled very well in metagenomes due to shared regions among 16S genes. Using single-copy marker genes to build genome trees has become increasingly popular for uncultivated species.
10p
vilarryellison
29-10-2021
9
1
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Transposable elements (TEs) are mobile DNA sequences known as drivers of genome evolution. Their impacts have been widely studied in animals, plants and insects, but little is known about them in microalgae. In a previous study, we compared the genetic polymorphisms between strains of the haptophyte microalga Tisochrysis lutea and suggested the involvement of active autonomous TEs in their genome evolution.
14p
vibeauty
23-10-2021
12
1
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Here we improved the reconstruction of HCMV full genomes by means of a hybrid, de novo genome-assembly bioinformatics pipeline upon data generated from the recently released MinION MkI B sequencer from Oxford Nanopore Technologies.
12p
vitzuyu2711
29-09-2021
17
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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Recent adva1nces in whole genome sequencing (WGS) based technologies have facilitated multi-step applications for predicting antimicrobial resistance (AMR) and investigating the molecular epidemiology of Neisseria gonorrhoeae.
11p
visilicon2711
20-08-2021
23
1
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The draft genome assemblies produced by new sequencing technologies present important challenges for automatic gene prediction pipelines, leading to less accurate gene models. New benchmark methods are needed to evaluate the accuracy of gene prediction methods in the face of incomplete genome assemblies, low genome coverage and quality, complex gene structures, or a lack of suitable sequences for evidence-based annotations.
20p
vijeeni2711
24-07-2021
13
0
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Hybrid genome assembly approaches leverage benefits of both long, relatively error-prone reads from third-generation sequencing technologies and short, accurate reads from secondgeneration sequencing technologies, to produce more accurate and contiguous de novo genome assemblies in comparison to using either technology independently.
15p
vilichoo2711
25-06-2021
15
1
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This paper presents a new continuous element model for studying the dynamic behavior of complex tubes composed by cylindrical shell, annular plate and conical shell which are widely used in automobile exhausts, sewer pipes and pipelines. Based on the analytical solutions of the system of differential equations for cylinders, cones and annular plates, the dynamic stiffness matrix for complex composite tubes has been established and assembled.
6p
cothumenhmong11
10-05-2021
17
1
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This paper presents the study results on the fabrication of a structural integrity assessment apparatus by determining stress concentration zones in pressure pipeline and equipment. The apparatus uses a triaxial magnetic field sensor to measure magnetic field components in three axes Ox, Oy, and Oz, in the working range of the magnetic field from -300 µT to 300 µT.
7p
kequaidan9
22-12-2020
13
1
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The use of short reads from High Throughput Sequencing (HTS) techniques is now commonplace in de novo assembly. Yet, obtaining contiguous assemblies from short reads is challenging, thus making scaffolding an important step in the assembly pipeline.
11p
vikentucky2711
26-11-2020
12
1
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Next-generation sequencing (NGS) has greatly facilitated metagenomic analysis but also raised new challenges for metagenomic DNA sequence assembly, owing to its high-throughput nature and extremely short reads generated by sequencers such as Illumina.
14p
vikentucky2711
24-11-2020
9
2
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