Computational problems of analysis of short next generation sequencing reads
Short read next generation sequencing (NGS) has significant impacts on modern genomics, genetics, cell biology and medicine, especially on meta-genomics, comparative genomics, polymorphism detection, mutation screening, transcriptome profiling, methylation profiling, chromatin remodelling and many m...
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| Format: | Article |
| Language: | English |
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2017-02-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/845 |
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| author | R. te Boekhorst F. M. Naumenko N. G. Orlova E. R. Galieva A. M. Spitsina I. V. Chadaeva Y. L. Orlov I. I. Abnizova |
| author_facet | R. te Boekhorst F. M. Naumenko N. G. Orlova E. R. Galieva A. M. Spitsina I. V. Chadaeva Y. L. Orlov I. I. Abnizova |
| author_sort | R. te Boekhorst |
| collection | DOAJ |
| description | Short read next generation sequencing (NGS) has significant impacts on modern genomics, genetics, cell biology and medicine, especially on meta-genomics, comparative genomics, polymorphism detection, mutation screening, transcriptome profiling, methylation profiling, chromatin remodelling and many more applications. However, NGS are prone for errors which complicate scientific conclusions. NGS technologies consist of shearing DNA molecules into collection of numerous small fragments, called a ‘library’, and their further extensive parallel sequencing. These sequenced overlapping fragments are called ‘reads’, they are assembled into contiguous strings. The contiguous sequences are in turn assembled into genomes for further analysis. Computational sequencing problems are those arising from numerical processing of sequenced samples. The numerical processing involves procedures such as: quality-scoring, mapping/assembling, and surprisingly, error-correction of a data. This paper is reviewing post-processing errors and computational methods to discern them. It also includes sequencing dictionary. We present here quality control of raw data, errors arising at the steps of alignment of sequencing reads to a reference genome and assembly. Finally this work presents identification of mutations (“Variant calling”) in sequencing data and its quality control. |
| format | Article |
| id | doaj-art-6f75b5e5c2cf4ac08e0ba331824284c8 |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2017-02-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-6f75b5e5c2cf4ac08e0ba331824284c82025-02-01T09:58:03ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592017-02-0120674675510.18699/VJ16.191537Computational problems of analysis of short next generation sequencing readsR. te Boekhorst0F. M. Naumenko1N. G. Orlova2E. R. Galieva3A. M. Spitsina4I. V. Chadaeva5Y. L. Orlov6I. I. Abnizova7University of HertfordshireNovosibirsk State UniversityNovosibirsk State University Novosibirsk State University of Architecture and Civil Engineering (Sibstrin)Novosibirsk State University Institute of Cytology and Genetics SB RASNovosibirsk State UniversityNovosibirsk State UniversityNovosibirsk State University Institute of Cytology and Genetics SB RASWellcome Trust Sanger InstituteShort read next generation sequencing (NGS) has significant impacts on modern genomics, genetics, cell biology and medicine, especially on meta-genomics, comparative genomics, polymorphism detection, mutation screening, transcriptome profiling, methylation profiling, chromatin remodelling and many more applications. However, NGS are prone for errors which complicate scientific conclusions. NGS technologies consist of shearing DNA molecules into collection of numerous small fragments, called a ‘library’, and their further extensive parallel sequencing. These sequenced overlapping fragments are called ‘reads’, they are assembled into contiguous strings. The contiguous sequences are in turn assembled into genomes for further analysis. Computational sequencing problems are those arising from numerical processing of sequenced samples. The numerical processing involves procedures such as: quality-scoring, mapping/assembling, and surprisingly, error-correction of a data. This paper is reviewing post-processing errors and computational methods to discern them. It also includes sequencing dictionary. We present here quality control of raw data, errors arising at the steps of alignment of sequencing reads to a reference genome and assembly. Finally this work presents identification of mutations (“Variant calling”) in sequencing data and its quality control.https://vavilov.elpub.ru/jour/article/view/845next generation sequencing (ngs)dnasequencing technologiesstatistical biasesgenome polymorphismssequencing errorsreview |
| spellingShingle | R. te Boekhorst F. M. Naumenko N. G. Orlova E. R. Galieva A. M. Spitsina I. V. Chadaeva Y. L. Orlov I. I. Abnizova Computational problems of analysis of short next generation sequencing reads Вавиловский журнал генетики и селекции next generation sequencing (ngs) dna sequencing technologies statistical biases genome polymorphisms sequencing errors review |
| title | Computational problems of analysis of short next generation sequencing reads |
| title_full | Computational problems of analysis of short next generation sequencing reads |
| title_fullStr | Computational problems of analysis of short next generation sequencing reads |
| title_full_unstemmed | Computational problems of analysis of short next generation sequencing reads |
| title_short | Computational problems of analysis of short next generation sequencing reads |
| title_sort | computational problems of analysis of short next generation sequencing reads |
| topic | next generation sequencing (ngs) dna sequencing technologies statistical biases genome polymorphisms sequencing errors review |
| url | https://vavilov.elpub.ru/jour/article/view/845 |
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