MutScan: fast detection and visualization of target mutations by scanning FASTQ data
Abstract Background Some types of clinical genetic tests, such as cancer testing using circulating tumor DNA (ctDNA), require sensitive detection of known target mutations. However, conventional next-generation sequencing (NGS) data analysis pipelines typically involve different steps of filtering,...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2018-01-01
|
| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12859-018-2024-6 |
| _version_ | 1818526160660725760 |
|---|---|
| author | Shifu Chen Tanxiao Huang Tiexiang Wen Hong Li Mingyan Xu Jia Gu |
| author_facet | Shifu Chen Tanxiao Huang Tiexiang Wen Hong Li Mingyan Xu Jia Gu |
| author_sort | Shifu Chen |
| collection | DOAJ |
| description | Abstract Background Some types of clinical genetic tests, such as cancer testing using circulating tumor DNA (ctDNA), require sensitive detection of known target mutations. However, conventional next-generation sequencing (NGS) data analysis pipelines typically involve different steps of filtering, which may cause miss-detection of key mutations with low frequencies. Variant validation is also indicated for key mutations detected by bioinformatics pipelines. Typically, this process can be executed using alignment visualization tools such as IGV or GenomeBrowse. However, these tools are too heavy and therefore unsuitable for validating mutations in ultra-deep sequencing data. Result We developed MutScan to address problems of sensitive detection and efficient validation for target mutations. MutScan involves highly optimized string-searching algorithms, which can scan input FASTQ files to grab all reads that support target mutations. The collected supporting reads for each target mutation will be piled up and visualized using web technologies such as HTML and JavaScript. Algorithms such as rolling hash and bloom filter are applied to accelerate scanning and make MutScan applicable to detect or visualize target mutations in a very fast way. Conclusion MutScan is a tool for the detection and visualization of target mutations by only scanning FASTQ raw data directly. Compared to conventional pipelines, this offers a very high performance, executing about 20 times faster, and offering maximal sensitivity since it can grab mutations with even one single supporting read. MutScan visualizes detected mutations by generating interactive pile-ups using web technologies. These can serve to validate target mutations, thus avoiding false positives. Furthermore, MutScan can visualize all mutation records in a VCF file to HTML pages for cloud-friendly VCF validation. MutScan is an open source tool available at GitHub: https://github.com/OpenGene/MutScan |
| first_indexed | 2024-12-11T06:19:03Z |
| format | Article |
| id | doaj.art-3e1f51b48bf44b7bad24258b16a3a606 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-11T06:19:03Z |
| publishDate | 2018-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-3e1f51b48bf44b7bad24258b16a3a6062022-12-22T01:17:53ZengBMCBMC Bioinformatics1471-21052018-01-0119111110.1186/s12859-018-2024-6MutScan: fast detection and visualization of target mutations by scanning FASTQ dataShifu Chen0Tanxiao Huang1Tiexiang Wen2Hong Li3Mingyan Xu4Jia Gu5Shenzhen Institutes of Advanced Technology, Chinese Academy of SciencesHaploX BiotechnologyShenzhen Institutes of Advanced Technology, Chinese Academy of SciencesHaploX BiotechnologyHaploX BiotechnologyShenzhen Institutes of Advanced Technology, Chinese Academy of SciencesAbstract Background Some types of clinical genetic tests, such as cancer testing using circulating tumor DNA (ctDNA), require sensitive detection of known target mutations. However, conventional next-generation sequencing (NGS) data analysis pipelines typically involve different steps of filtering, which may cause miss-detection of key mutations with low frequencies. Variant validation is also indicated for key mutations detected by bioinformatics pipelines. Typically, this process can be executed using alignment visualization tools such as IGV or GenomeBrowse. However, these tools are too heavy and therefore unsuitable for validating mutations in ultra-deep sequencing data. Result We developed MutScan to address problems of sensitive detection and efficient validation for target mutations. MutScan involves highly optimized string-searching algorithms, which can scan input FASTQ files to grab all reads that support target mutations. The collected supporting reads for each target mutation will be piled up and visualized using web technologies such as HTML and JavaScript. Algorithms such as rolling hash and bloom filter are applied to accelerate scanning and make MutScan applicable to detect or visualize target mutations in a very fast way. Conclusion MutScan is a tool for the detection and visualization of target mutations by only scanning FASTQ raw data directly. Compared to conventional pipelines, this offers a very high performance, executing about 20 times faster, and offering maximal sensitivity since it can grab mutations with even one single supporting read. MutScan visualizes detected mutations by generating interactive pile-ups using web technologies. These can serve to validate target mutations, thus avoiding false positives. Furthermore, MutScan can visualize all mutation records in a VCF file to HTML pages for cloud-friendly VCF validation. MutScan is an open source tool available at GitHub: https://github.com/OpenGene/MutScanhttp://link.springer.com/article/10.1186/s12859-018-2024-6MutScanMutation scanVariant visualizationFast detection |
| spellingShingle | Shifu Chen Tanxiao Huang Tiexiang Wen Hong Li Mingyan Xu Jia Gu MutScan: fast detection and visualization of target mutations by scanning FASTQ data BMC Bioinformatics MutScan Mutation scan Variant visualization Fast detection |
| title | MutScan: fast detection and visualization of target mutations by scanning FASTQ data |
| title_full | MutScan: fast detection and visualization of target mutations by scanning FASTQ data |
| title_fullStr | MutScan: fast detection and visualization of target mutations by scanning FASTQ data |
| title_full_unstemmed | MutScan: fast detection and visualization of target mutations by scanning FASTQ data |
| title_short | MutScan: fast detection and visualization of target mutations by scanning FASTQ data |
| title_sort | mutscan fast detection and visualization of target mutations by scanning fastq data |
| topic | MutScan Mutation scan Variant visualization Fast detection |
| url | http://link.springer.com/article/10.1186/s12859-018-2024-6 |
| work_keys_str_mv | AT shifuchen mutscanfastdetectionandvisualizationoftargetmutationsbyscanningfastqdata AT tanxiaohuang mutscanfastdetectionandvisualizationoftargetmutationsbyscanningfastqdata AT tiexiangwen mutscanfastdetectionandvisualizationoftargetmutationsbyscanningfastqdata AT hongli mutscanfastdetectionandvisualizationoftargetmutationsbyscanningfastqdata AT mingyanxu mutscanfastdetectionandvisualizationoftargetmutationsbyscanningfastqdata AT jiagu mutscanfastdetectionandvisualizationoftargetmutationsbyscanningfastqdata |