Duesselpore: a full-stack local web server for rapid and simple analysis of Oxford Nanopore Sequencing data

2021 ◽  
Author(s):  
Christian Vogeley ◽  
Thach Nguyen ◽  
Selina Woeste ◽  
Jean Krutmann ◽  
Thomas Haarmann-Stemmann ◽  
...  
Keyword(s):  
Data Analysis ◽  
Molecular Mechanisms ◽  
Cost Effective ◽  
Sequencing Data ◽  
Bioinformatic Tools ◽  
Cellular Processes ◽  
Aryl Hydrocarbon ◽  
Gene Concept ◽  
Oxford Nanopore ◽  
Ngs Data

Genome-wide analysis of transcriptomes offers extensive insights into the molecular mechanisms underlying the physiology of all known species and discover those that are still hidden. Oxford Nanopore Technologies (ONT) has recently been developed as a fast, miniaturized, portable and a cost effective alternative to Next Generation Sequencing. However, RNA-seq data analysis software that exploit ONT portability and allows scientists to easily analyze ONT data everywhere without bioinformatic expertise is not widely available. We developed DuesselporeTM, an easy-to-follow deep sequencing workflow that runs as a local webserver and allows the analysis of ONT data everywhere without requiring additional bioinformatic tools or internet connection. DuesselporeTM output includes differentially expressed genes and further downstream analyses, such as variance heatmap, disease and gene ontology plots, gene concept network plots and exports customized pathways for different cellular processes. We validated DuesselporeTM by analyzing the transcriptomic changes induced by PCB126, a dioxin-like PCB and a potent aryl hydrocarbon receptor (AhR) agonist in human HaCaT keratinocytes, a well characterized model system. DuesselporeTM was specifically developed to analyze ONT data but we also implemented NGS data analysis. DuesselporeTM is compatible with Microsoft and Mac operating systems, allows convenient, reliable and cost-effective analysis of ONT and NGS data.

miND pipeline AWS EC2 installation and setup v2

2022 ◽  
Author(s):  
Andreas B Diendorfer ◽  
Kseniya.Khamina not provided ◽  
marianne.pultar not provided
Keyword(s):  
Data Analysis ◽  
Public Repository ◽  
Sequencing Data ◽  
Analysis Pipeline ◽  
Ngs Data Analysis ◽  
Ngs Data ◽  
Data Analysis Pipeline

miND is a NGS data analysis pipeline for smallRNA sequencing data. In this protocol, the pipeline is setup and run on an AWS EC2 instance with example data from a public repository. Please see the publication paper on F1000 for more details on the pipeline and how to use it.

scholarly journals rANOMALY: AmplicoN wOrkflow for Microbial community AnaLYsis

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 7
Author(s):  
Sebastien Theil ◽  
Etienne Rifa
Keyword(s):  
Data Analysis ◽  
Microbial Community ◽  
Statistical Tests ◽  
Marker Gene ◽  
R Package ◽  
Microbial Community Analysis ◽  
Differential Analysis ◽  
Sequencing Data ◽  
Statistical Validation ◽  
Bioinformatic Tools

Bioinformatic tools for marker gene sequencing data analysis are continuously and rapidly evolving, thus integrating most recent techniques and tools is challenging. We present an R package for data analysis of 16S and ITS amplicons based sequencing. This workflow is based on several R functions and performs automatic treatments from fastq sequence files to diversity and differential analysis with statistical validation. The main purpose of this package is to automate bioinformatic analysis, ensure reproducibility between projects, and to be flexible enough to quickly integrate new bioinformatic tools or statistical methods. rANOMALY is an easy to install and customizable R package, that uses amplicon sequence variants (ASV) level for microbial community characterization. It integrates all assets of the latest bioinformatics methods, such as better sequence tracking, decontamination from control samples, use of multiple reference databases for taxonomic annotation, all main ecological analysis for which we propose advanced statistical tests, and a cross-validated differential analysis by four different methods. Our package produces ready to publish figures, and all of its outputs are made to be integrated in Rmarkdown code to produce automated reports.

scholarly journals CoMA – an intuitive and user-friendly pipeline for amplicon-sequencing data analysis

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243241
Author(s):  
Sebastian Hupfauf ◽  
Mohammad Etemadi ◽  
Marina Fernández-Delgado Juárez ◽  
María Gómez-Brandón ◽  
Heribert Insam ◽  
...  
Keyword(s):  
Operating System ◽  
Data Analysis ◽  
Amplicon Sequencing ◽  
Sequencing Data ◽  
Taxonomic Assignment ◽  
Benchmark Test ◽  
Next Generation Sequencing Ngs ◽  
User Friendly ◽  
Ngs Data ◽  
Mock Communities

In recent years, there has been a veritable boost in next-generation sequencing (NGS) of gene amplicons in biological and medical studies. Huge amounts of data are produced and need to be analyzed adequately. Various online and offline analysis tools are available; however, most of them require extensive expertise in computer science or bioinformatics, and often a Linux-based operating system. Here, we introduce “CoMA–Comparative Microbiome Analysis” as a free and intuitive analysis pipeline for amplicon-sequencing data, compatible with any common operating system. Moreover, the tool offers various useful services including data pre-processing, quality checking, clustering to operational taxonomic units (OTUs), taxonomic assignment, data post-processing, data visualization, and statistical appraisal. The workflow results in highly esthetic and publication-ready graphics, as well as output files in standardized formats (e.g. tab-delimited OTU-table, BIOM, NEWICK tree) that can be used for more sophisticated analyses. The CoMA output was validated by a benchmark test, using three mock communities with different sample characteristics (primer set, amplicon length, diversity). The performance was compared with that of Mothur, QIIME and QIIME2-DADA2, popular packages for NGS data analysis. Furthermore, the functionality of CoMA is demonstrated on a practical example, investigating microbial communities from three different soils (grassland, forest, swamp). All tools performed well in the benchmark test and were able to reveal the majority of all genera in the mock communities. Also for the soil samples, the results of CoMA were congruent to those of the other pipelines, in particular when looking at the key microbial players.

scholarly journals Pathophysiological Roles of Stress-Activated Protein Kinases in Pulmonary Fibrosis

2021 ◽  
Vol 22 (11) ◽  
pp. 6041
Author(s):  
Yoshitoshi Kasuya ◽  
Jun-Dal Kim ◽  
Masahiko Hatano ◽  
Koichiro Tatsumi ◽  
Shuichi Matsuda
Keyword(s):  
Pulmonary Fibrosis ◽  
Protein Kinases ◽  
Molecular Mechanisms ◽  
Alveolar Epithelial Cells ◽  
Mitogen Activated Protein Kinase ◽  
Sequencing Data ◽  
Alveolar Epithelial ◽  
Cellular Processes ◽  
Mitogen Activated Protein ◽  
Fibrotic Lung Diseases

Idiopathic pulmonary fibrosis (IPF) is one of the most symptomatic progressive fibrotic lung diseases, in which patients have an extremely poor prognosis. Therefore, understanding the precise molecular mechanisms underlying pulmonary fibrosis is necessary for the development of new therapeutic options. Stress-activated protein kinases (SAPKs), c-Jun N-terminal kinase (JNK), and p38 mitogen-activated protein kinase (p38) are ubiquitously expressed in various types of cells and activated in response to cellular environmental stresses, including inflammatory and apoptotic stimuli. Type II alveolar epithelial cells, fibroblasts, and macrophages are known to participate in the progression of pulmonary fibrosis. SAPKs can control fibrogenesis by regulating the cellular processes and molecular functions in various types of lung cells (including cells of the epithelium, interstitial connective tissue, blood vessels, and hematopoietic and lymphoid tissue), all aspects of which remain to be elucidated. We recently reported that the stepwise elevation of intrinsic p38 signaling in the lungs is correlated with a worsening severity of bleomycin-induced fibrosis, indicating an importance of this pathway in the progression of pulmonary fibrosis. In addition, a transcriptome analysis of RNA-sequencing data from this unique model demonstrated that several lines of mechanisms are involved in the pathogenesis of pulmonary fibrosis, which provides a basis for further studies. Here, we review the accumulating evidence for the spatial and temporal roles of SAPKs in pulmonary fibrosis.

scholarly journals Comparison of long-read methods for sequencing and assembly of a plant genome

GigaScience ◽  
2020 ◽  
Vol 9 (12) ◽  
Author(s):  
Valentine Murigneux ◽  
Subash Kumar Rai ◽  
Agnelo Furtado ◽  
Timothy J C Bruxner ◽  
Wei Tian ◽  
...  
Keyword(s):  
De Novo ◽  
Cost Effective ◽  
Genome Project ◽  
Plant Genome ◽  
Sequencing Data ◽  
Pacific Biosciences ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Long Read ◽  
The Cost

Abstract Background Sequencing technologies have advanced to the point where it is possible to generate high-accuracy, haplotype-resolved, chromosome-scale assemblies. Several long-read sequencing technologies are available, and a growing number of algorithms have been developed to assemble the reads generated by those technologies. When starting a new genome project, it is therefore challenging to select the most cost-effective sequencing technology, as well as the most appropriate software for assembly and polishing. It is thus important to benchmark different approaches applied to the same sample. Results Here, we report a comparison of 3 long-read sequencing technologies applied to the de novo assembly of a plant genome, Macadamia jansenii. We have generated sequencing data using Pacific Biosciences (Sequel I), Oxford Nanopore Technologies (PromethION), and BGI (single-tube Long Fragment Read) technologies for the same sample. Several assemblers were benchmarked in the assembly of Pacific Biosciences and Nanopore reads. Results obtained from combining long-read technologies or short-read and long-read technologies are also presented. The assemblies were compared for contiguity, base accuracy, and completeness, as well as sequencing costs and DNA material requirements. Conclusions The 3 long-read technologies produced highly contiguous and complete genome assemblies of M. jansenii. At the time of sequencing, the cost associated with each method was significantly different, but continuous improvements in technologies have resulted in greater accuracy, increased throughput, and reduced costs. We propose updating this comparison regularly with reports on significant iterations of the sequencing technologies.

scholarly journals GLM-based optimization of NGS data analysis: A case study of Roche 454, Ion Torrent PGM and Illumina NextSeq sequencing data

PLoS ONE ◽  
2017 ◽  
Vol 12 (2) ◽  
pp. e0171983 ◽  
Author(s):  
Sarah Sandmann ◽  
Aniek O. de Graaf ◽  
Bert A. van der Reijden ◽  
Joop H. Jansen ◽  
Martin Dugas
Keyword(s):  
Data Analysis ◽  
Ion Torrent ◽  
Sequencing Data ◽  
Ion Torrent Pgm ◽  
Ngs Data Analysis ◽  
Ngs Data ◽  
Roche 454

scholarly journals Real-time demultiplexing Nanopore barcoded sequencing data with npBarcode

2017 ◽  
Author(s):  
Son Hoang Nguyen ◽  
Tania Duarte ◽  
Lachlan J. M. Coin ◽  
Minh Duc Cao
Keyword(s):  
Real Time ◽  
Nanopore Sequencing ◽  
Sequencing Data ◽  
Analysis Pipeline ◽  
Bioinformatic Tools ◽  
Oxford Nanopore ◽  
Pooled Sequencing ◽  
Cross Platform ◽  
Real Time Applications ◽  
Friendly Graphical User Interface

AbstractMotivationThe recently introduced barcoding protocol to Oxford Nanopore sequencing has increased the versatility of the technology. Several bioinformatic tools have been developed to demultiplex the barcoded reads, but none of them support the streaming analysis. This limits the use of pooled sequencing in real-time applications, which is one of the main advantages of the technology.ResultsWe introduced npBarcode, an open source and cross platform tool for barcode demultiplex in streaming fashion. npBarcode can be seamlessly integrated into a streaming analysis pipeline. The tool also provides a friendly graphical user interface through npReader, allowing the real-time visual monitoring of the sequencing progress of barcoded samples. We show that npBarcode achieves comparable accuracies to the other alternatives.AvailabilitynpBarcode is bundled in Japsa - a Java tools kit for genome analysis, and is freely available at https://github.com/hsnguyen/npBarcode.

scholarly journals Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis

2020 ◽  
Author(s):  
Kristoffer Sahlin ◽  
Botond Sipos ◽  
Phillip L James ◽  
Paul Medvedev
Keyword(s):  
Error Correction ◽  
Transcriptome Analysis ◽  
Transcription Initiation ◽  
Cost Effective ◽  
Error Rates ◽  
Computational Method ◽  
Bias Error ◽  
Sequencing Data ◽  
Oxford Nanopore ◽  
Long Read

AbstractOxford Nanopore (ONT) is a leading long-read technology which has been revolutionizing transcriptome analysis through its capacity to sequence the majority of transcripts from end-to-end. This has greatly increased our ability to study the diversity of transcription mechanisms such as transcription initiation, termination, and alternative splicing. However, ONT still suffers from high error rates which have thus far limited its scope to reference-based analyses. When a reference is not available or is not a viable option due to reference-bias, error correction is a crucial step towards the reconstruction of the sequenced transcripts and downstream sequence analysis of transcripts. In this paper, we present a novel computational method to error correct ONT cDNA sequencing data, called isONcorrect. IsONcorrect is able to jointly use all isoforms from a gene during error correction, thereby allowing it to correct reads at low sequencing depths. We are able to obtain a median accuracy of 98.9-99.6%, demonstrating the feasibility of applying cost-effective cDNA full transcript length sequencing for reference-free transcriptome analysis.

miND pipeline AWS EC2 installation and setup v1

2021 ◽  
Author(s):  
Andreas B B Diendorfer ◽  
Kseniya.Khamina not provided ◽  
marianne.pultar not provided
Keyword(s):  
Data Analysis ◽  
Public Repository ◽  
Sequencing Data ◽  
Analysis Pipeline ◽  
Ngs Data Analysis ◽  
Ngs Data ◽  
Data Analysis Pipeline

miND is a NGS data analysis pipeline for smallRNA sequencing data. In this protocol, the pipeline is setup and run on an AWS EC2 instance with example data from a public repository. Please see the publication paper on F1000 for more details on the pipeline and how to use it.

scholarly journals Comparison of long read methods for sequencing and assembly of a plant genome

2020 ◽  
Author(s):  
Valentine Murigneux ◽  
Subash Kumar Rai ◽  
Agnelo Furtado ◽  
Timothy J.C. Bruxner ◽  
Wei Tian ◽  
...  
Keyword(s):  
De Novo ◽  
Cost Effective ◽  
Genome Project ◽  
Plant Genome ◽  
Sequencing Data ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Long Read ◽  
The Cost ◽  
Genome Assemblies

AbstractSequencing technologies have advanced to the point where it is possible to generate high accuracy, haplotype resolved, chromosome scale assemblies. Several long read sequencing technologies are available on the market and a growing number of algorithms have been developed over the last years to assemble the reads generated by those technologies. When starting a new genome project, it is therefore challenging to select the most cost-effective sequencing technology as well as the most appropriate software for assembly and polishing. For this reason, it is important to benchmark different approaches applied to the same sample. Here, we report a comparison of three long read sequencing technologies applied to the de novo assembly of a plant genome, Macadamia jansenii. We have generated sequencing data using Pacific Biosciences (Sequel I), Oxford Nanopore Technologies (PromethION) and BGI (single-tube Long Fragment Read) technologies for the same sample. Several assemblers were benchmarked in the assembly of PacBio and Nanopore reads. Results obtained from combining long read technologies or short read and long read technologies are also presented. The assemblies were compared for contiguity, accuracy and completeness as well as sequencing costs and DNA material requirements. Overall, the three long read technologies produced highly contiguous and complete genome assemblies of Macadamia jansenii. At the time of sequencing, the cost associated with each method was significantly different but continuous improvements in technologies have resulted in greater accuracy, increased throughput and reduced costs. We propose updating this comparison regularly with reports on significant iterations of the sequencing technologies.

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