Abstract:
:The Next-Generation Sequencing (NGS) platforms provide a major approach to obtaining millions of short reads from samples. NGS has been used in a wide range of analyses, such as for determining genome sequences, analyzing evolutionary processes, identifying gene expression and resolving metagenomic analyses. Usually, the quality of NGS data impacts the final study conclusions. Moreover, quality assessment is generally considered the first step in data analyses to ensure the use of only reliable reads for further studies. In NGS platforms, the presence of duplicated reads (redundancy) that are usually introduced during library sequencing is a major issue. These might have a serious impact on research application, as redundancies in reads can lead to difficulties in subsequent analysis (e.g., de novo genome assembly). Herein, we present NGSReadsTreatment, a computational tool for the removal of duplicated reads in paired-end or single-end datasets. NGSReadsTreatment can handle reads from any platform with the same or different sequence lengths. Using the probabilistic structure Cuckoo Filter, the redundant reads are identified and removed by comparing the reads with themselves. Thus, no prerequisite is required beyond the set of reads. NGSReadsTreatment was compared with other redundancy removal tools in analyzing different sets of reads. The results demonstrated that NGSReadsTreatment was better than the other tools in both the amount of redundancies removed and the use of computational memory for all analyses performed. Available in https://sourceforge.net/projects/ngsreadstreatment/ .
journal_name
Sci Repjournal_title
Scientific reportsauthors
Gaia ASC,de Sá PHCG,de Oliveira MS,Veras AAOdoi
10.1038/s41598-019-48242-wsubject
Has Abstractpub_date
2019-08-12 00:00:00pages
11681issue
1issn
2045-2322pii
10.1038/s41598-019-48242-wjournal_volume
9pub_type
杂志文章abstract::Coherent B2-ordered NiAl-type precipitates have been used to reinforce solid-solution body-centered-cubic iron for high-temperature application in fossil-energy power plants. In this study, we investigate the stability of nano-sized precipitates in a NiAl-strengthened ferritic alloy at 700-950 °C using ultra-small ang...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep16081
更新日期:2015-11-05 00:00:00
abstract::Autonomic dysfunction as a partial contributing factor to cardiovascular instability in jaundiced patients is often associated with increased serum bilirubin levels. Whether increased serum bilirubin levels could directly inhibit sympathetic ganglion transmission by blocking neuronal nicotinic acetylcholine receptors ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep07475
更新日期:2014-12-15 00:00:00
abstract::Because of the lack of cell wall, Micoplasma species require a fine control of membrane fluidity and integrity. mg517 is an essential gene of Mycoplasma genitalium responsible for the biosynthesis of membrane glycoglycerolipids. It encodes for a unique glycosyltransferase (MG517) with processive activity, transferring...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-42970-9
更新日期:2019-05-08 00:00:00
abstract::The prion protein (PrPC), a mainly neuronal protein, is known to modulate glucose homeostasis in mouse models. We explored the underlying mechanism in mouse models and the human pancreatic β-cell line 1.1B4. We report expression of PrPC on mouse pancreatic β-cells, where it promoted uptake of iron through divalent-met...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-24786-1
更新日期:2018-04-26 00:00:00
abstract::By moving the alkoxy group on the spacer from position 5 to position 4 to add another protocol for the algorithm for intermolecular and intramolecular hydrogen bonding interactions, highly regioselectivity of noncovalent synthesis of the hydrazide-based cyclic hexamers was achieved: one out of thirteen possible isomer...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep01059
更新日期:2013-01-01 00:00:00
abstract::The Acer truncatum Bunge is a particular widespread forest tree species in northern China. VLCFAs are important to eukaryotes survival and play diverse roles throughout the development. So far, there are reports that the Acer truncatum seeds fatty acid (FA) rich in VLCFAs, but little is known about the physiological m...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-33999-3
更新日期:2018-10-19 00:00:00
abstract::Nanomaterials are being extensively produced and applied in society. Human and environmental exposures are, therefore, inevitable and so increased attention is being given to nanotoxicity. While silica nanoparticles (NP) are one of the top five nanomaterials found in consumer and biomedical products, their toxicity pr...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep37145
更新日期:2016-11-22 00:00:00
abstract::Cellvibrio mixtus strain J3-8 is a gram-negative, xylanase-producing aerobic soil bacterium isolated from giant snails in Singapore. It is able to produce up to 10.1 U ml(-1) of xylanase, which is comparable to xylanase production from known bacterial and fungal strains. Genome sequence analysis of strain J3-8 reveals...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep10521
更新日期:2015-05-21 00:00:00
abstract::Determination of the absolute configrations for natural products is one of the most important and challenging tasks, especially when the molecules display high conformational flexibility. In this paper, eight new prenylxanthones, aspergixanthones A-H (1-8), and one known analogue (9), were isolated from the marine-der...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-28996-5
更新日期:2018-07-13 00:00:00
abstract::Cells harboring latent HIV-1 pose a major obstacle to eradication of the virus. The 'shock and kill' strategy has been broadly explored to purge the latent reservoir; however, none of the current latency-reversing agents (LRAs) can safely and effectively activate the latent virus in patients. In this study, we report ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-07157-0
更新日期:2017-08-25 00:00:00
abstract::Recent studies have shown that cellular metabolism plays an important role in regulating immune cell functions. In immune cell differentiation, both interleukin-17-producing T (Th17) cells and dendritic cells (DCs) exhibit increased glycolysis through the upregulation of glycolytic enzymes, such as hexokinase-2 (HK2)....
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep42412
更新日期:2017-02-10 00:00:00
abstract::Multiple parasitic arthropods of medical importance depend on symbiotic bacteria. While the link between scabies and secondary bacterial infections causing post infective complications of Group A streptococcal and staphylococcal pyoderma is increasingly recognized, very little is known about the microbiota of Sarcopte...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-47892-0
更新日期:2019-08-13 00:00:00
abstract::Deer are an iconic group of large mammals that originated in the Early Miocene of Eurasia (ca. 19 Ma). While there is some consensus on key relationships among their members, on the basis of molecular- or morphology-based analyses, or combined approaches, many questions remain, and the bony labyrinth has shown conside...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-12848-9
更新日期:2017-10-13 00:00:00
abstract::This study was to investigate effects of progesterone vaginal sustained-release gel and intramuscular injection of progesterone on frozen-thawed embryos transfer in 3013 patients receiving vaginal progesterone sustained-release gel and progesterone injection in artificial cycle for frozen-thawed embryo transfer. All p...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-51717-5
更新日期:2019-10-24 00:00:00
abstract::Landau-Zener (LZ) transition has received renewed interest as an alternative approach to control single-qubit states. An LZ transition occurs when a system passes through an avoided crossing that arises from quantum mechanical coupling of two levels, taking the system to a coherent superposition of the two states. The...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-23468-2
更新日期:2018-04-03 00:00:00
abstract::Hesperiidae is one of the largest families of butterflies. Our knowledge of the higher systematics on hesperiids from China is still very limited. We infer the phylogenetic relationships of the subfamilies of Chinese skippers based on three mitochondrial genes (cytochrome b (Cytb), the NADH dehydrogenase subunit 1 (ND...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep11140
更新日期:2015-06-10 00:00:00
abstract::Due to their convergent evolution, dogs have been suggested as a good model for the evolution of human social skills, such as tolerance and cooperativeness. However, recent studies have revealed that wolves (dogs' closest undomesticated relatives) are more tolerant and cooperative with conspecifics than dogs. It is st...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-40468-y
更新日期:2019-03-07 00:00:00
abstract::The emergence of single-cell RNA sequencing (scRNA-seq) technologies has enabled us to measure the expression levels of thousands of genes at single-cell resolution. However, insufficient quantities of starting RNA in the individual cells cause significant dropout events, introducing a large number of zero counts in t...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-34688-x
更新日期:2018-11-05 00:00:00
abstract::Biomaterial development for tissue engineering applications is rapidly increasing but necessitates efficacy and safety testing prior to clinical application. Current in vitro and in vivo models hold a number of limitations, including expense, lack of correlation between animal models and human outcomes and the need to...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep32168
更新日期:2016-08-31 00:00:00
abstract::Mixed Plasmodium malaria infections can lead to severe malaria. This systematic review and meta-analysis aimed to explore the prevalence of severe mixed Plasmodium malaria infection and to compare it with the prevalence of severe P. falciparum malaria mono-infection across the included studies. Original English-langua...
journal_title:Scientific reports
pub_type: 杂志文章,meta分析
doi:10.1038/s41598-020-68082-3
更新日期:2020-07-06 00:00:00
abstract::The objective of this study was to determine if Ihh is required for fracture healing. Fibular fracture was created in adult Col2a1-CreERT2; Ihhfl/fl mice. Ihhfl/fl mice received Tamoxifen (TM) to delete Ihh. WT mice received Cyclopamine to inhibit Hh pathway. Callus tissue properties and Ihh pathway were analyzed at 1...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-28657-7
更新日期:2018-07-09 00:00:00
abstract::High-grade gliomas are the most aggressive malignant brain tumors. Accurate pre-operative prognosis for this cohort can lead to better treatment planning. Conventional survival prediction based on clinical information is subjective and could be inaccurate. Recent radiomics studies have shown better prognosis by using ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-37387-9
更新日期:2019-01-31 00:00:00
abstract::Baeyer-Villiger monooxygenases (BVMOs) can be used for the biosynthesis of lactones and esters from ketones. However, the BVMO-based biocatalysts are not so stable under process conditions. Thereby, this study focused on enhancing stability of the BVMO-based biocatalysts. The biotransformation of ricinoleic acid into ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-28575-8
更新日期:2018-07-06 00:00:00
abstract::Small ruminants, including sheep and goats are natural hosts of scrapie, and the progression of scrapie pathogenesis is strongly influenced by polymorphisms in the prion protein gene (PRNP). Although Korean native goats have been consumed as meat and health food, the evaluation of the susceptibility to scrapie in thes...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-51621-y
更新日期:2019-10-25 00:00:00
abstract::A high-resolution genetic map is a useful tool for assaying genomic structural variation and clarifying the evolution of polyploid cotton. A total of 36956 SSRs, including 11289 released in previous studies and 25567 which were newly developed based on the genome sequences of G. arboreum and G. raimondii, were utilize...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-08006-w
更新日期:2017-08-09 00:00:00
abstract::Majority of novel X-ray crystal structures of proteins are currently solved using the anomalous diffraction signal provided by selenium after incorporation of selenomethionine instead of natural methionine by genetic engineering methods. However, selenium can be inserted into protein crystals in the form of selenourea...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep37123
更新日期:2016-11-14 00:00:00
abstract::Bipolar disorder (BD) is a debilitating mental disorder that cannot be diagnosed by objective laboratory-based modalities. Our previous studies have independently used nuclear magnetic resonance (NMR)-based and gas chromatography-mass spectrometry (GC-MS)-based metabonomic methods to characterize the urinary metabolic...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep05855
更新日期:2014-07-28 00:00:00
abstract::Grain boundary (GB) oxidation of proton-irradiated 304 nuclear grade stainless steel in primary water of pressurized water reactor was investigated. The investigation was conducted by studying microstructure of the oxide and oxide precursor formed at GB on an "atom-by-atom" basis by a combination of atom-probe tomogra...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-80600-x
更新日期:2021-01-14 00:00:00
abstract::Local communities are assembled from larger-scale species pools via dispersal, environmental filtering, biotic interactions, and local stochastic demographic processes. The relative importance, scaling and interplay of these assembly processes can be elucidated by comparing local communities to variously circumscribed...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep09337
更新日期:2015-03-23 00:00:00
abstract::Microbial rhodopsin is a photoreceptor protein found in various bacteria and archaea, and it is considered to be a light-utilization device unique to heterotrophs. Recent studies have shown that several cyanobacterial genomes also include genes that encode rhodopsins, indicating that these auxiliary light-utilizing pr...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-73606-y
更新日期:2020-10-07 00:00:00