scholarly journals ECCsplorer: a pipeline to detect extrachromosomal circular DNA (eccDNA) from next-generation sequencing data

2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Ludwig Mann ◽  
Kathrin M. Seibt ◽  
Beatrice Weber ◽  
Tony Heitkam
Keyword(s):  
Next Generation Sequencing ◽  
Transposable Elements ◽  
Data Availability ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Bioinformatics Pipeline ◽  
Circular Dna ◽  
Wide Range ◽  
Generation Sequencing

Abstract Background Extrachromosomal circular DNAs (eccDNAs) are ring-like DNA structures physically separated from the chromosomes with 100 bp to several megabasepairs in size. Apart from carrying tandemly repeated DNA, eccDNAs may also harbor extra copies of genes or recently activated transposable elements. As eccDNAs occur in all eukaryotes investigated so far and likely play roles in stress, cancer, and aging, they have been prime targets in recent research—with their investigation limited by the scarcity of computational tools. Results Here, we present the ECCsplorer, a bioinformatics pipeline to detect eccDNAs in any kind of organism or tissue using next-generation sequencing techniques. Following Illumina-sequencing of amplified circular DNA (circSeq), the ECCsplorer enables an easy and automated discovery of eccDNA candidates. The data analysis encompasses two major procedures: first, read mapping to the reference genome allows the detection of informative read distributions including high coverage, discordant mapping, and split reads. Second, reference-free comparison of read clusters from amplified eccDNA against control sample data reveals specifically enriched DNA circles. Both software parts can be run separately or jointly, depending on the individual aim or data availability. To illustrate the wide applicability of our approach, we analyzed semi-artificial and published circSeq data from the model organisms Homo sapiens and Arabidopsis thaliana, and generated circSeq reads from the non-model crop plant Beta vulgaris. We clearly identified eccDNA candidates from all datasets, with and without reference genomes. The ECCsplorer pipeline specifically detected mitochondrial mini-circles and retrotransposon activation, showcasing the ECCsplorer’s sensitivity and specificity. Conclusion The ECCsplorer (available online at https://github.com/crimBubble/ECCsplorer) is a bioinformatics pipeline to detect eccDNAs in any kind of organism or tissue using next-generation sequencing data. The derived eccDNA targets are valuable for a wide range of downstream investigations—from analysis of cancer-related eccDNAs over organelle genomics to identification of active transposable elements.

scholarly journals ECCsplorer: a pipeline to detect extrachromosomal circular DNA (eccDNA) from next-generation sequencing data

2021 ◽  
Author(s):  
Ludwig Mann ◽  
Kathrin M. Seibt ◽  
Beatrice Weber ◽  
Tony Heitkam
Keyword(s):  
Next Generation Sequencing ◽  
Transposable Elements ◽  
Control Sample ◽  
Data Availability ◽  
Next Generation Sequencing Data ◽  
Model Organisms ◽  
Next Generation ◽  
Circular Dna ◽  
Wide Range ◽  
Generation Sequencing

Motivation: Extrachromosomal circular DNAs (eccDNAs) are ring-like DNA structures physically separated from the chromosomes with 100 bp to several megabasepairs in size. Apart from carrying tandemly repeated DNA, eccDNAs may also harbor extra copies of genes or recently activated transposable elements. As eccDNAs occur in all eukaryotes investigated so far and likely play roles in stress, cancer, and aging, they have been prime targets in recent research - with their investigation limited by the scarcity of computational tools. Results: Here, we present the ECCsplorer, a bioinformatics pipeline to detect eccDNAs in any kind of organism or tissue using next-generation sequencing techniques. Following Illumina-sequencing of amplified circular DNA (circSeq), the ECCsplorer enables an easy and automated discovery of eccDNA candidates. The data analysis encompasses two major procedures: First, read mapping to the reference genome allows the detection of informative read distributions including high coverage, discordant mapping, and split reads. Second, reference-free comparison of read clusters from amplified eccDNA against control sample data reveals specifically enriched DNA circles. Both software parts can be run separately or jointly, depending on the individual aim or data availability. To illustrate the wide applicability of our approach, we analyzed semi-artificial and published circSeq data from the model organisms H. sapiens and A. thaliana, and generated circSeq reads from the non-model crop B. vulgaris. We clearly identified eccDNA candidates from all datasets, with and without reference genomes. The ECCsplorer pipeline specifically detected mitochondrial mini-circles and retrotransposon activation, showcasing the ECCsplorer's sensitivity and specificity. The derived eccDNA targets are valuable for a wide range of downstream investigations - from analysis of cancer-related eccDNAs over organelle genomics to identification of active transposable elements. Availability and implementation: The ECCsplorer pipeline is available on GitHub at https://github.de/crimBubble/ECCsplorer under the GNU license.

scholarly journals A bioinformatics pipeline for rare genetic diseases in South African patients

2019 ◽  
Vol 115 (3/4) ◽  
Author(s):  
Maryke Schoonen ◽  
Albertus S. Seyffert ◽  
Francois H. van Der Westhuizen ◽  
Izelle Smuts
Keyword(s):  
South Africa ◽  
Next Generation Sequencing ◽  
South African ◽  
Rare Diseases ◽  
Next Generation Sequencing Data ◽  
Common Disease ◽  
Next Generation ◽  
Sequencing Data ◽  
Bioinformatics Pipeline ◽  
Generation Sequencing

The research fields of bioinformatics and computational biology are growing rapidly in South Africa. Bioinformatics pipelines play an integral part in handling sequencing data, which are used to investigate the aetiology of common and rare diseases. Bioinformatics platforms for common disease aetiology are well supported and continuously being developed in South Africa. However, the same is not the case for rare diseases aetiology research. Investigations into the latter rely on international cloud-based tools for data analyses and ultimately confirmation of a genetic disease. However, these tools are not necessarily optimised for ethnically diverse population groups. We present an in-house developed bioinformatics pipeline to enable researchers to annotate and filter variants in either exome or amplicon next-generation sequencing data. This pipeline was developed using next-generation sequencing data of a predominantly African cohort of patients diagnosed with rare disease. Significance: We demonstrate the feasibility of in-country development of ethnicity-sensitive, automated bioinformatics pipelines using free software in a South African context. We provide a roadmap for development of similarly ethnicity-sensitive bioinformatics pipelines.

scholarly journals T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data

2014 ◽  
Author(s):  
Anna-Sophie Fiston-Lavier ◽  
Maite G. Barrón ◽  
Dmitri A. Petrov ◽  
Josefa González
Keyword(s):  
Next Generation Sequencing ◽  
Transposable Elements ◽  
Frequency Estimation ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Flexible Tool ◽  
Depth Analysis ◽  
Individual Strain ◽  
Generation Sequencing

Transposable elements (TEs) constitute the most active, diverse and ancient component in a broad range of genomes. Complete understanding of genome function and evolution cannot be achieved without a thorough understanding of TE impact and biology. However, in-depth analysis of TEs still represents a challenge due to the repetitive nature of these genomic entities. In this work, we present a broadly applicable and flexible tool: T-lex2. T-lex2 is the only available software that allows routine, automatic, and accurate genotyping of individual TE insertions and estimation of their population frequencies both using individual strain and pooled next-generation sequencing (NGS) data. Furthermore, T-lex2 also assesses the quality of the calls allowing the identification of miss-annotated TEs and providing the necessary information to re-annotate them. The flexible and customizable design of T-lex2 allows running it in any genome and for any type of TE insertion. Here, we tested the fidelity of T-lex2 using the fly and human genomes. Overall, T-lex2 represents a significant improvement in our ability to analyze the contribution of TEs to genome function and evolution as well as learning about the biology of TEs. T-lex2 is freely available online at http://sourceforge.net/projects/tlex/.

scholarly journals Development and validation of Houston Methodist Variant Viewer version 3: updates to our application for interpretation of next-generation sequencing data

JAMIA Open ◽  
2020 ◽  
Vol 3 (2) ◽  
pp. 299-305
Author(s):  
Paul A Christensen ◽  
Sishir Subedi ◽  
Kristi Pepper ◽  
Heather L Hendrickson ◽  
Zejuan Li ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Data Entry ◽  
Computation Time ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Bioinformatics Pipeline ◽  
System Maintenance ◽  
Development And Validation ◽  
Generation Sequencing

Abstract Objectives Informatics tools that support next-generation sequencing workflows are essential to deliver timely interpretation of somatic variants in cancer. Here, we describe significant updates to our laboratory developed bioinformatics pipelines and data management application termed Houston Methodist Variant Viewer (HMVV). Materials and Methods We collected feature requests and workflow improvement suggestions from the end-users of HMVV version 1. Over 1.5 years, we iteratively implemented these features in five sequential updates to HMVV version 3. Results We improved the performance and data throughput of the application while reducing the opportunity for manual data entry errors. We enabled end-user workflows for pipeline monitoring, variant interpretation and annotation, and integration with our laboratory information system. System maintenance was improved through enhanced defect reporting, heightened data security, and improved modularity in the code and system environments. Discussion and Conclusion Validation of each HMVV update was performed according to expert guidelines. We enabled an 8× reduction in the bioinformatics pipeline computation time for our longest running assay. Our molecular pathologists can interpret the assay results at least 2 days sooner than was previously possible. The application and pipeline code are publicly available at https://github.com/hmvv.

scholarly journals DNAscan: a fast, computationally and memory efficient bioinformatics pipeline for the analysis of DNA next-generation-sequencing data

2018 ◽  
Author(s):  
A Iacoangeli ◽  
A Al Khleifat ◽  
W Sproviero ◽  
A Shatunov ◽  
AR Jones ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
High Performance ◽  
Genetic Material ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Bioinformatics Pipeline ◽  
Bioinformatics Tools ◽  
Ngs Data ◽  
Generation Sequencing

AbstractThe generation of DNA Next Generation Sequencing (NGS) data is a commonly applied approach for studying the genetic basis of biological processes, including diseases, and underpins the aspirations of precision medicine. However, there are significant challenges when dealing with NGS data. A huge number of bioinformatics tools exist and it is therefore challenging to design an analysis pipeline; NGS analysis is computationally intensive, requiring expensive infrastructure which can be problematic given that many medical and research centres do not have adequate high performance computing facilities and the use of cloud computing facilities is not always possible due to privacy and ownership issues. We have therefore developed a fast and efficient bioinformatics pipeline that allows for the analysis of DNA sequencing data, while requiring little computational effort and memory usage. We achieved this by exploiting state-of-the-art bioinformatics tools. DNAscan can analyse raw, 40x whole genome NGS data in 8 hours, using as little as 8 threads and 16 Gbs of RAM, while guaranteeing a high performance. DNAscan can look for SNVs, small indels, SVs, repeat expansions and viral genetic material (or any other organism). Its results are annotated using a customisable variety of databases including ClinVar, Exac and dbSNP, and a local deployment of the gene.iobio platform is available for an on-the-fly result visualisation.

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