scholarly journals NeatSeq-Flow: A Lightweight High Throughput Sequencing Workflow Platform for Non-Programmers and Programmers alike

2017 ◽  
Author(s):  
Menachem Sklarz ◽  
Liron Levin ◽  
Michal Gordon ◽  
Vered Chalifa-Caspi
Keyword(s):  
Real Time ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Computer Clusters ◽  
Execution Monitoring ◽  
Software Packages ◽  
Generic Module ◽  
Programming Knowledge ◽  
Python Programming ◽  
Bioinformatics Workflows

AbstractNowadays, it has become almost a necessity for many biologists to execute bioinformatics workflows (WFs) as part of their research. However, most WF-management software packages require for their operation at least some programming expertise. Here we describe NeatSeq-Flow, a platform that enables users with no programming knowledge to design and execute complex high throughput sequencing WFs. This is achieved by using a compendium of pre-built modules as well as a generic module, both do not require programming expertise. Nonetheless, NeatSeq-Flow retains the flexibility to generate sophisticated WF modules using templates and only basic Python programming abilities. NeatSeq-Flow is designed to enable easy sharing of WFs and modules by conceptually separating modules, WF design, sample information and execution. Moreover, NeatSeq-Flow works hand in hand with CONDA environments for easy installation of the WF’s analysis programs in one go. NeatSeq-Flow enables efficient WF execution on computer clusters by parallelizing on both samples and WF steps. NeatSeq-Flow operates by shell-script generation; thus it allows full transparency of the WF process. NeatSeq-Flow offers real-time WF execution monitoring, detailed documentation and self-sustaining WF backups for reproducibility. All of these features make NeatSeq-Flow an easy-to-use WF platform while not compromising for flexibility, reproducibility, transparency and efficiency.Availabilityhttp://neatseq-flow.readthedocs.io/en/latest/[email protected]

scholarly journals A real-time decoding sequencing technology—new possibility for high throughput sequencing

RSC Advances ◽  
2017 ◽  
Vol 7 (64) ◽  
pp. 40141-40151
Author(s):  
Dan Pu ◽  
Pengfeng Xiao
Keyword(s):  
Real Time ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Sequencing Technology

The challenges and corresponding solutions for a decoding sequencing to be compatible with high throughput sequencing (HTS) technologies are provided.

Identifying transcriptional miRNA biomarkers by integrating high-throughput sequencing and real-time PCR data

Methods ◽  
2013 ◽  
Vol 59 (1) ◽  
pp. 154-163 ◽  
Author(s):  
Sven Rahmann ◽  
Marcel Martin ◽  
Johannes H. Schulte ◽  
Johannes Köster ◽  
Tobias Marschall ◽  
...  
Keyword(s):  
Real Time ◽  
High Throughput ◽  
Real Time Pcr ◽  
High Throughput Sequencing

scholarly journals Verification of miRNAs in ginseng decoction by high-throughput sequencing and quantitative real-time PCR

Heliyon ◽  
2019 ◽  
Vol 5 (4) ◽  
pp. e01418 ◽  
Author(s):  
Yingfang Wang ◽  
Mengyuan Peng ◽  
Wenjuan Wang ◽  
Yanlin Chen ◽  
Zhihua He ◽  
...  
Keyword(s):  
Real Time ◽  
High Throughput ◽  
Real Time Pcr ◽  
High Throughput Sequencing ◽  
Quantitative Real Time Pcr

scholarly journals Effect of Ag Nanoparticles on Denitrification and Microbial Community in a Paddy Soil

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiao Zhang ◽  
Di Dang ◽  
Lingsi Zheng ◽  
Lingyu Wu ◽  
Yu Wu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Real Time ◽  
Quantitative Pcr ◽  
High Throughput ◽  
Paddy Soil ◽  
Ag Nanoparticles ◽  
High Throughput Sequencing ◽  
Emission Rate ◽  
Rrna Gene ◽  
Real Time Quantitative Pcr

The extensive application of Ag nanoparticles (AgNPs) in industry, agriculture, and food processing areas increases the possibility of its release and accumulation to agroecosystem, but the effects of AgNPs to denitrification and the microbial community in paddy ecosystems are still poorly studied. In this study, microcosmic simulation experiments were established to investigate the response of soil denitrification to different levels of AgNPs (i.e., 0.1, 1, 10, and 50 mg/kg) in a paddy soil. Real-time quantitative PCR and high-throughput sequencing were conducted to reveal the microbial mechanism of the nanometer effect. The results showed that, though 0.1–10 mg/kg AgNPs had no significant effects on denitrification rate and N2O emission rate compared to CK and bulk Ag treatments, 50 mg/kg AgNPs significantly stimulated more than 60% increase of denitrification rate and N2O emission rate on the 3rd day (P < 0.05). Real-time quantitative PCR revealed that 50 mg/kg AgNPs significantly decreased the abundance of 16S bacterial rRNA gene, nirS/nirK, cnorB, and nosZ genes, but it did not change the narG gene abundance. The correlation analysis further revealed that the cumulative N2O emission was positively correlated with the ratio of all the five tested denitrifying genes to bacterial 16S rRNA gene (P < 0.05), indicating that the tolerance of narG gene to AgNPs was the key factor of the increase in denitrification in the studied soil. High-throughput sequencing showed that only the 50-mg/kg-AgNP treatment significantly changed the microbial community composition compared to bulk Ag and CK treatments. The response of microbial phylotypes to AgNPs suggested that the most critical bacteria which drove the stimulation of 50 mg/kg AgNPs on N2O emission were Firmicutes and β-proteobacteria, such as Clotridiales, Burkholderiales, and Anaerolineales. This study revealed the effects of AgNPs to denitrification in a paddy ecosystem and could provide a scientific basis for understanding of the environmental and toxicological effects of Ag nanomaterials.

Comparing high throughput sequencing and real time qPCR for characterizing entomopathogenic nematode biogeography

2020 ◽  
Vol 145 ◽  
pp. 107793 ◽  
Author(s):  
Alexandros Dritsoulas ◽  
Raquel Campos-Herrera ◽  
Rubén Blanco-Pérez ◽  
Larry W. Duncan
Keyword(s):  
Real Time ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Entomopathogenic Nematode ◽  
Real Time Qpcr

scholarly journals On the optimal trimming of high-throughput mRNA sequence data

2013 ◽  
Author(s):  
Matthew D. MacManes
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Deep Understanding ◽  
Sequencing Technologies ◽  
Software Packages ◽  
Sequencing Quality ◽  
Functional Biology ◽  
Genome Level ◽  
Optimal Strength

AbstractThe widespread and rapid adoption of high-throughput sequencing technologies has afforded researchers the opportunity to gain a deep understanding of genome level processes that underlie evolutionary change, and perhaps more importantly, the links between genotype and phenotype. In particular, researchers interested in functional biology and adaptation have used these technologies to sequence mRNA transcriptomes of specific tissues, which in turn are often compared to other tissues, or other individuals with different phenotypes. While these techniques are extremely powerful, careful attention to data quality is required. In particular, because high-throughput sequencing is more error-prone than traditional Sanger sequencing, quality trimming of sequence reads should be an important step in all data processing pipelines. While several software packages for quality trimming exist, no general guidelines for the specifics of trimming have been developed. Here, using empirically derived sequence data, I provide general recommendations regarding the optimal strength of trimming, specifically in mRNA-Seq studies. Although very aggressive quality trimming is common, this study suggests that a more gentle trimming, specifically of those nucleotides whose Phred score <2 or <5, is optimal for most studies across a wide variety of metrics.

scholarly journals Quality control of the traditional Chinese medicine Ruyi jinhuang powder based on high-throughput sequencing and real-time PCR

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Qiang Li ◽  
Ying Sun ◽  
Huijun Guo ◽  
Feng Sang ◽  
Hongyu Ma ◽  
...  
Keyword(s):  
Quality Control ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Real Time ◽  
High Throughput ◽  
Real Time Pcr ◽  
High Throughput Sequencing

scholarly journals Automated genotyping of microsatellite loci from feces with high throughput sequences

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0258906
Author(s):  
Isabel Salado ◽  
Alberto Fernández-Gil ◽  
Carles Vilà ◽  
Jennifer A. Leonard
Keyword(s):  
Next Generation Sequencing ◽  
High Throughput ◽  
Microsatellite Loci ◽  
High Throughput Sequencing ◽  
Individual Identification ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Software Packages ◽  
Generation Sequencing

Ecological and conservation genetic studies often use noninvasive sampling, especially with elusive or endangered species. Because microsatellites are generally short in length, they can be amplified from low quality samples such as feces. Microsatellites are highly polymorphic so few markers are enough for reliable individual identification, kinship determination, or population characterization. However, the genotyping process from feces is expensive and time consuming. Given next-generation sequencing (NGS) and recent software developments, automated microsatellite genotyping from NGS data may now be possible. These software packages infer the genotypes directly from sequence reads, increasing throughput. Here we evaluate the performance of four software packages to genotype microsatellite loci from Iberian wolf (Canis lupus) feces using NGS. We initially combined 46 markers in a single multiplex reaction for the first time, of which 19 were included in the final analyses. Megasat was the software that provided genotypes with fewer errors. Coverage over 100X provided little additional information, but a relatively high number of PCR replicates were necessary to obtain a high quality genotype from highly unoptimized, multiplexed reactions (10 replicates for 18 of the 19 loci analyzed here). This could be reduced through optimization. The use of new bioinformatic tools and next-generation sequencing data to genotype these highly informative markers may increase throughput at a reasonable cost and with a smaller amount of laboratory work. Thus, high throughput sequencing approaches could facilitate the use of microsatellites with fecal DNA to address ecological and conservation questions.

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