scholarly journals SequencEnG: an Interactive Knowledge Base of Sequencing Techniques

2018 ◽  
Author(s):  
Yi Zhang ◽  
Mohith Manjunath ◽  
Yeonsung Kim ◽  
Joerg Heintz ◽  
Jun S. Song
Keyword(s):  
Knowledge Base ◽  
Educational Resource ◽  
Rapid Progress ◽  
Structured Knowledge ◽  
Ngs Data Analysis ◽  
Next Generation Sequencing Ngs ◽  
User Friendly ◽  
Ngs Data ◽  
Generation Sequencing ◽  
Acute Challenge

AbstractNext-generation sequencing (NGS) techniques are revolutionizing biomedical research by providing powerful methods for generating genomic and epigenomic profiles. The rapid progress is posing an acute challenge to students and researchers to stay acquainted with the numerous available methods. We have developed an interactive online educational resource called SequencEnG (acronym for Sequencing Techniques Engine for Genomics) to provide a tree-structured knowledge base of 66 different sequencing techniques and step-by-step NGS data analysis pipelines comparing popular tools. SequencEnG is designed to facilitate barrier-free learning of current NGS techniques and provides a user-friendly interface for searching through experimental and analysis methods. SequencEnG is part of the project KnowEnG (Knowledge Engine for Genomics) and is freely available at http://education.knoweng.org/sequenceng/.

scholarly journals Patient Derived Xenografts for Genome-Driven Therapy of Osteosarcoma

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 416
Author(s):  
Lorena Landuzzi ◽  
Maria Cristina Manara ◽  
Pier-Luigi Lollini ◽  
Katia Scotlandi
Keyword(s):  
Clinical Trials ◽  
Tumor Heterogeneity ◽  
Functional Studies ◽  
Ngs Data Analysis ◽  
The Many ◽  
Orthotopic Xenografts ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing ◽  
Somatic Copy Number Alterations

Osteosarcoma (OS) is a rare malignant primary tumor of mesenchymal origin affecting bone. It is characterized by a complex genotype, mainly due to the high frequency of chromothripsis, which leads to multiple somatic copy number alterations and structural rearrangements. Any effort to design genome-driven therapies must therefore consider such high inter- and intra-tumor heterogeneity. Therefore, many laboratories and international networks are developing and sharing OS patient-derived xenografts (OS PDX) to broaden the availability of models that reproduce OS complex clinical heterogeneity. OS PDXs, and new cell lines derived from PDXs, faithfully preserve tumor heterogeneity, genetic, and epigenetic features and are thus valuable tools for predicting drug responses. Here, we review recent achievements concerning OS PDXs, summarizing the methods used to obtain ectopic and orthotopic xenografts and to fully characterize these models. The availability of OS PDXs across the many international PDX platforms and their possible use in PDX clinical trials are also described. We recommend the coupling of next-generation sequencing (NGS) data analysis with functional studies in OS PDXs, as well as the setup of OS PDX clinical trials and co-clinical trials, to enhance the predictive power of experimental evidence and to accelerate the clinical translation of effective genome-guided therapies for this aggressive disease.

scholarly journals FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files

2018 ◽  
Author(s):  
Leandro Gabriel Roser ◽  
Fernán Agüero ◽  
Daniel Oscar Sánchez
Keyword(s):  
Quality Control ◽  
Data Analysis ◽  
The Novel ◽  
Web Environment ◽  
Ngs Data Analysis ◽  
Novel Concept ◽  
Next Generation Sequencing Ngs ◽  
User Friendly ◽  
Ngs Data ◽  
Analysis Platform

AbstractBackgroundExploration and processing of FASTQ files are the first steps in state-of-the-art data analysis workflows of Next Generation Sequencing (NGS) platforms. The large amount of data generated by these technologies has put a challenge in terms of rapid analysis and visualization of sequencing information. Recent integration of the R data analysis platform with web visual frameworks has stimulated the development of user-friendly, powerful, and dynamic NGS data analysis applications.ResultsThis paper presents FastqCleaner, a Bioconductor visual application for both quality-control (QC) and pre-processing of FASTQ files. The interface shows diagnostic information for the input and output data and allows to select a series of filtering and trimming operations in an interactive framework. FastqCleaner combines the technology of Bioconductor for NGS data analysis with the data visualization advantages of a web environment.ConclusionsFastqCleaner is an user-friendly, offline-capable tool that enables access to advanced Bioconductor infrastructure. The novel concept of a Bioconductor interactive application that can be used without the need for programming skills, makes FastqCleaner a valuable resource for NGS data analysis.

scholarly journals CSI NGS Portal: An Online Platform for Automated NGS Data Analysis and Sharing

2020 ◽  
Vol 21 (11) ◽  
pp. 3828
Author(s):  
Omer An ◽  
Kar-Tong Tan ◽  
Ying Li ◽  
Jia Li ◽  
Chan-Shuo Wu ◽  
...  
Keyword(s):  
Data Analysis ◽  
Final Report ◽  
Online Platform ◽  
Fastq Format ◽  
Health And Disease ◽  
Ngs Data Analysis ◽  
Next Generation Sequencing Ngs ◽  
User Friendly ◽  
Ngs Data

Next-generation sequencing (NGS) has been a widely-used technology in biomedical research for understanding the role of molecular genetics of cells in health and disease. A variety of computational tools have been developed to analyse the vastly growing NGS data, which often require bioinformatics skills, tedious work and a significant amount of time. To facilitate data processing steps minding the gap between biologists and bioinformaticians, we developed CSI NGS Portal, an online platform which gathers established bioinformatics pipelines to provide fully automated NGS data analysis and sharing in a user-friendly website. The portal currently provides 16 standard pipelines for analysing data from DNA, RNA, smallRNA, ChIP, RIP, 4C, SHAPE, circRNA, eCLIP, Bisulfite and scRNA sequencing, and is flexible to expand with new pipelines. The users can upload raw data in FASTQ format and submit jobs in a few clicks, and the results will be self-accessible via the portal to view/download/share in real-time. The output can be readily used as the final report or as input for other tools depending on the pipeline. Overall, CSI NGS Portal helps researchers rapidly analyse their NGS data and share results with colleagues without the aid of a bioinformatician. The portal is freely available at: https://csibioinfo.nus.edu.sg/csingsportal.

scholarly journals Discovering Selected Antibodies From Deep-Sequenced Phage-Display Antibody Library Using ATTILA

2020 ◽  
Vol 14 ◽  
pp. 117793222091524 ◽  
Author(s):  
Andréa Queiroz Maranhão ◽  
Heidi Muniz Silva ◽  
Waldeyr Mendes Cordeiro da Silva ◽  
Renato Kaylan Alves França ◽  
Thais Canassa De Leo ◽  
...  
Keyword(s):  
Phage Display ◽  
Fold Change ◽  
Robust Solution ◽  
Performance Accuracy ◽  
Variable Domains ◽  
Ngs Data Analysis ◽  
Complementarity Determining Regions ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

Phage display is a powerful technique to select high-affinity antibodies for different purposes, including biopharmaceuticals. Next-generation sequencing (NGS) presented itself as a robust solution, making it possible to assess billions of sequences of the variable domains from selected sublibraries. Handling this process, a central difficulty is to find the selected clones. Here, we present the AutomaTed Tool For Immunoglobulin Analysis (ATTILA), a new tool to analyze and find the enriched variable domains throughout a biopanning experiment. The ATTILA is a workflow that combines publicly available tools and in-house programs and scripts to find the fold-change frequency of deeply sequenced amplicons generated from selected VH and VL domains. We analyzed the same human Fab library NGS data using ATTILA in 5 different experiments, as well as on 2 biopanning experiments regarding performance, accuracy, and output. These analyses proved to be suitable to assess library variability and to list the more enriched variable domains, as ATTILA provides a report with the amino acid sequence of each identified domain, along with its complementarity-determining regions (CDRs), germline classification, and fold change. Finally, the methods employed here demonstrated a suitable manner to combine amplicon generation and NGS data analysis to discover new monoclonal antibodies (mAbs).

scholarly journals sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs

2021 ◽  
Author(s):  
Andrea Di Gioacchino ◽  
Rachel Legendre ◽  
Yannis Rahou ◽  
Valerie Najburg ◽  
Pierre Charneau ◽  
...  
Keyword(s):  
Regulatory Sequences ◽  
Accessory Proteins ◽  
Viral Genomes ◽  
Bioinformatic Tools ◽  
Subgenomic Rnas ◽  
Next Generation Sequencing Ngs ◽  
User Friendly ◽  
Ngs Data ◽  
Initial Knowledge ◽  
Generation Sequencing

Coronavirus RNA-dependent RNA polymerases produce subgenomic RNAs (sgRNAs) that encode viral structural and accessory proteins. User-friendly bioinformatic tools to detect and quantify sgRNA production are urgently needed to study the growing number of next-generation sequencing (NGS) data of SARS-CoV-2. We introduced sgDI-tector to identify and quantify sgRNA in SARS-CoV-2 NGS data. sgDI-tector allowed detection of sgRNA without initial knowledge of the transcription-regulatory sequences. We produced NGS data and successfully detected the nested set of sgRNAs with the ranking M>ORF3a>N>ORF6>ORF7a>ORF8>S>E>ORF7b. We also compared the level of sgRNA production with other types of viral RNA products such as defective interfering viral genomes.

scholarly journals Easymap: A User-Friendly Software Package for Rapid Mapping-by-Sequencing of Point Mutations and Large Insertions

2021 ◽  
Vol 12 ◽  
Author(s):  
Samuel Daniel Lup ◽  
David Wilson-Sánchez ◽  
Sergio Andreu-Sánchez ◽  
José Luis Micol
Keyword(s):  
Point Mutations ◽  
Rapid Identification ◽  
Graphical Interface ◽  
Rna Seq ◽  
Source Program ◽  
Next Generation Sequencing Ngs ◽  
User Friendly ◽  
Ngs Data ◽  
Mapping By Sequencing ◽  
Generation Sequencing

Mapping-by-sequencing strategies combine next-generation sequencing (NGS) with classical linkage analysis, allowing rapid identification of the causal mutations of the phenotypes exhibited by mutants isolated in a genetic screen. Computer programs that analyze NGS data obtained from a mapping population of individuals derived from a mutant of interest to identify a causal mutation are available; however, the installation and usage of such programs requires bioinformatic skills, modifying or combining pieces of existing software, or purchasing licenses. To ease this process, we developed Easymap, an open-source program that simplifies the data analysis workflows from raw NGS reads to candidate mutations. Easymap can perform bulked segregant mapping of point mutations induced by ethyl methanesulfonate (EMS) with DNA-seq or RNA-seq datasets, as well as tagged-sequence mapping for large insertions, such as transposons or T-DNAs. The mapping analyses implemented in Easymap have been validated with experimental and simulated datasets from different plant and animal model species. Easymap was designed to be accessible to all users regardless of their bioinformatics skills by implementing a user-friendly graphical interface, a simple universal installation script, and detailed mapping reports, including informative images and complementary data for assessment of the mapping results. Easymap is available at http://genetics.edu.umh.es/resources/easymap; its Quickstart Installation Guide details the recommended procedure for installation.

scholarly journals sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs

RNA ◽  
2021 ◽  
pp. rna.078969.121
Author(s):  
Andrea Di Gioacchino ◽  
Rachel Legendre ◽  
Yannis Rahou ◽  
Valérie Najburg ◽  
Pierre Charneau ◽  
...  
Keyword(s):  
Regulatory Sequences ◽  
Accessory Proteins ◽  
Viral Genomes ◽  
Bioinformatic Tools ◽  
Subgenomic Rnas ◽  
Next Generation Sequencing Ngs ◽  
User Friendly ◽  
Ngs Data ◽  
Initial Knowledge ◽  
Generation Sequencing

Coronavirus RNA-dependent RNA polymerases produce subgenomic RNAs (sgRNAs) that encode viral structural and accessory proteins. User-friendly bioinformatic tools to detect and quantify sgRNA production are urgently needed to study the growing number of next-generation sequencing (NGS) data of SARS-CoV-2. We introduced sgDI-tector to identify and quantify sgRNA in SARS-CoV-2 NGS data. sgDI-tector allowed detection of sgRNA without initial knowledge of the transcription-regulatory sequences. We produced NGS data and successfully detected the nested set of sgRNAs with the ranking M>ORF3a>N>ORF6>ORF7a>ORF8>S>E>ORF7b. We also compared the level of sgRNA production with other types of viral RNA products such as defective interfering viral genomes.

Sign in / Sign up

Export Citation Format

Share Document