Cargando…
SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing
BACKGROUND: Next-generation sequencers (NGSs) have become one of the main tools for current biology. To obtain useful insights from the NGS data, it is essential to control low-quality portions of the data affected by technical errors such as air bubbles in sequencing fluidics. RESULTS: We develop a...
Autores principales: | , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4133631/ https://www.ncbi.nlm.nih.gov/pubmed/25103311 http://dx.doi.org/10.1186/1471-2164-15-664 |
_version_ | 1782330768545021952 |
---|---|
author | Sato, Yukuto Kojima, Kaname Nariai, Naoki Yamaguchi-Kabata, Yumi Kawai, Yosuke Takahashi, Mamoru Mimori, Takahiro Nagasaki, Masao |
author_facet | Sato, Yukuto Kojima, Kaname Nariai, Naoki Yamaguchi-Kabata, Yumi Kawai, Yosuke Takahashi, Mamoru Mimori, Takahiro Nagasaki, Masao |
author_sort | Sato, Yukuto |
collection | PubMed |
description | BACKGROUND: Next-generation sequencers (NGSs) have become one of the main tools for current biology. To obtain useful insights from the NGS data, it is essential to control low-quality portions of the data affected by technical errors such as air bubbles in sequencing fluidics. RESULTS: We develop a software SUGAR (subtile-based GUI-assisted refiner) which can handle ultra-high-throughput data with user-friendly graphical user interface (GUI) and interactive analysis capability. The SUGAR generates high-resolution quality heatmaps of the flowcell, enabling users to find possible signals of technical errors during the sequencing. The sequencing data generated from the error-affected regions of a flowcell can be selectively removed by automated analysis or GUI-assisted operations implemented in the SUGAR. The automated data-cleaning function based on sequence read quality (Phred) scores was applied to a public whole human genome sequencing data and we proved the overall mapping quality was improved. CONCLUSION: The detailed data evaluation and cleaning enabled by SUGAR would reduce technical problems in sequence read mapping, improving subsequent variant analysis that require high-quality sequence data and mapping results. Therefore, the software will be especially useful to control the quality of variant calls to the low population cells, e.g., cancers, in a sample with technical errors of sequencing procedures. |
format | Online Article Text |
id | pubmed-4133631 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-41336312014-08-18 SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing Sato, Yukuto Kojima, Kaname Nariai, Naoki Yamaguchi-Kabata, Yumi Kawai, Yosuke Takahashi, Mamoru Mimori, Takahiro Nagasaki, Masao BMC Genomics Software BACKGROUND: Next-generation sequencers (NGSs) have become one of the main tools for current biology. To obtain useful insights from the NGS data, it is essential to control low-quality portions of the data affected by technical errors such as air bubbles in sequencing fluidics. RESULTS: We develop a software SUGAR (subtile-based GUI-assisted refiner) which can handle ultra-high-throughput data with user-friendly graphical user interface (GUI) and interactive analysis capability. The SUGAR generates high-resolution quality heatmaps of the flowcell, enabling users to find possible signals of technical errors during the sequencing. The sequencing data generated from the error-affected regions of a flowcell can be selectively removed by automated analysis or GUI-assisted operations implemented in the SUGAR. The automated data-cleaning function based on sequence read quality (Phred) scores was applied to a public whole human genome sequencing data and we proved the overall mapping quality was improved. CONCLUSION: The detailed data evaluation and cleaning enabled by SUGAR would reduce technical problems in sequence read mapping, improving subsequent variant analysis that require high-quality sequence data and mapping results. Therefore, the software will be especially useful to control the quality of variant calls to the low population cells, e.g., cancers, in a sample with technical errors of sequencing procedures. BioMed Central 2014-08-08 /pmc/articles/PMC4133631/ /pubmed/25103311 http://dx.doi.org/10.1186/1471-2164-15-664 Text en © Sato et al.; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Software Sato, Yukuto Kojima, Kaname Nariai, Naoki Yamaguchi-Kabata, Yumi Kawai, Yosuke Takahashi, Mamoru Mimori, Takahiro Nagasaki, Masao SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing |
title | SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing |
title_full | SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing |
title_fullStr | SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing |
title_full_unstemmed | SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing |
title_short | SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing |
title_sort | sugar: graphical user interface-based data refiner for high-throughput dna sequencing |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4133631/ https://www.ncbi.nlm.nih.gov/pubmed/25103311 http://dx.doi.org/10.1186/1471-2164-15-664 |
work_keys_str_mv | AT satoyukuto sugargraphicaluserinterfacebaseddatarefinerforhighthroughputdnasequencing AT kojimakaname sugargraphicaluserinterfacebaseddatarefinerforhighthroughputdnasequencing AT nariainaoki sugargraphicaluserinterfacebaseddatarefinerforhighthroughputdnasequencing AT yamaguchikabatayumi sugargraphicaluserinterfacebaseddatarefinerforhighthroughputdnasequencing AT kawaiyosuke sugargraphicaluserinterfacebaseddatarefinerforhighthroughputdnasequencing AT takahashimamoru sugargraphicaluserinterfacebaseddatarefinerforhighthroughputdnasequencing AT mimoritakahiro sugargraphicaluserinterfacebaseddatarefinerforhighthroughputdnasequencing AT nagasakimasao sugargraphicaluserinterfacebaseddatarefinerforhighthroughputdnasequencing |