MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS reads
Abstract Background The rapid advancement of next-generation sequencing (NGS) machines in terms of speed and affordability has led to the generation of a massive amount of biological data at the expense of data quality as errors become more prevalent. This introduces the need to utilize different ap...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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BMC
2024-02-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-024-05681-1 |
| _version_ | 1827325942321643520 |
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| author | Amira Sami Sara El-Metwally M. Z. Rashad |
| author_facet | Amira Sami Sara El-Metwally M. Z. Rashad |
| author_sort | Amira Sami |
| collection | DOAJ |
| description | Abstract Background The rapid advancement of next-generation sequencing (NGS) machines in terms of speed and affordability has led to the generation of a massive amount of biological data at the expense of data quality as errors become more prevalent. This introduces the need to utilize different approaches to detect and filtrate errors, and data quality assurance is moved from the hardware space to the software preprocessing stages. Results We introduce MAC-ErrorReads, a novel Machine learning-Assisted Classifier designed for filtering Erroneous NGS Reads. MAC-ErrorReads transforms the erroneous NGS read filtration process into a robust binary classification task, employing five supervised machine learning algorithms. These models are trained on features extracted through the computation of Term Frequency-Inverse Document Frequency (TF_IDF) values from various datasets such as E. coli, GAGE S. aureus, H. Chr14, Arabidopsis thaliana Chr1 and Metriaclima zebra. Notably, Naive Bayes demonstrated robust performance across various datasets, displaying high accuracy, precision, recall, F1-score, MCC, and ROC values. The MAC-ErrorReads NB model accurately classified S. aureus reads, surpassing most error correction tools with a 38.69% alignment rate. For H. Chr14, tools like Lighter, Karect, CARE, Pollux, and MAC-ErrorReads showed rates above 99%. BFC and RECKONER exceeded 98%, while Fiona had 95.78%. For the Arabidopsis thaliana Chr1, Pollux, Karect, RECKONER, and MAC-ErrorReads demonstrated good alignment rates of 92.62%, 91.80%, 91.78%, and 90.87%, respectively. For the Metriaclima zebra, Pollux achieved a high alignment rate of 91.23%, despite having the lowest number of mapped reads. MAC-ErrorReads, Karect, and RECKONER demonstrated good alignment rates of 83.76%, 83.71%, and 83.67%, respectively, while also producing reasonable numbers of mapped reads to the reference genome. Conclusions This study demonstrates that machine learning approaches for filtering NGS reads effectively identify and retain the most accurate reads, significantly enhancing assembly quality and genomic coverage. The integration of genomics and artificial intelligence through machine learning algorithms holds promise for enhancing NGS data quality, advancing downstream data analysis accuracy, and opening new opportunities in genetics, genomics, and personalized medicine research. |
| first_indexed | 2024-03-07T14:37:32Z |
| format | Article |
| id | doaj.art-18482c2efefe4070936b7505ec70b794 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-03-07T14:37:32Z |
| publishDate | 2024-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-18482c2efefe4070936b7505ec70b7942024-03-05T20:32:01ZengBMCBMC Bioinformatics1471-21052024-02-0125113010.1186/s12859-024-05681-1MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS readsAmira Sami0Sara El-Metwally1M. Z. Rashad2Department of Computer Science, Faculty of Computers and Information, Mansoura UniversityDepartment of Computer Science, Faculty of Computers and Information, Mansoura UniversityDepartment of Computer Science, Faculty of Computers and Information, Mansoura UniversityAbstract Background The rapid advancement of next-generation sequencing (NGS) machines in terms of speed and affordability has led to the generation of a massive amount of biological data at the expense of data quality as errors become more prevalent. This introduces the need to utilize different approaches to detect and filtrate errors, and data quality assurance is moved from the hardware space to the software preprocessing stages. Results We introduce MAC-ErrorReads, a novel Machine learning-Assisted Classifier designed for filtering Erroneous NGS Reads. MAC-ErrorReads transforms the erroneous NGS read filtration process into a robust binary classification task, employing five supervised machine learning algorithms. These models are trained on features extracted through the computation of Term Frequency-Inverse Document Frequency (TF_IDF) values from various datasets such as E. coli, GAGE S. aureus, H. Chr14, Arabidopsis thaliana Chr1 and Metriaclima zebra. Notably, Naive Bayes demonstrated robust performance across various datasets, displaying high accuracy, precision, recall, F1-score, MCC, and ROC values. The MAC-ErrorReads NB model accurately classified S. aureus reads, surpassing most error correction tools with a 38.69% alignment rate. For H. Chr14, tools like Lighter, Karect, CARE, Pollux, and MAC-ErrorReads showed rates above 99%. BFC and RECKONER exceeded 98%, while Fiona had 95.78%. For the Arabidopsis thaliana Chr1, Pollux, Karect, RECKONER, and MAC-ErrorReads demonstrated good alignment rates of 92.62%, 91.80%, 91.78%, and 90.87%, respectively. For the Metriaclima zebra, Pollux achieved a high alignment rate of 91.23%, despite having the lowest number of mapped reads. MAC-ErrorReads, Karect, and RECKONER demonstrated good alignment rates of 83.76%, 83.71%, and 83.67%, respectively, while also producing reasonable numbers of mapped reads to the reference genome. Conclusions This study demonstrates that machine learning approaches for filtering NGS reads effectively identify and retain the most accurate reads, significantly enhancing assembly quality and genomic coverage. The integration of genomics and artificial intelligence through machine learning algorithms holds promise for enhancing NGS data quality, advancing downstream data analysis accuracy, and opening new opportunities in genetics, genomics, and personalized medicine research.https://doi.org/10.1186/s12859-024-05681-1Next-generation sequencingError filtrationMachine learningClassificationFeature extraction |
| spellingShingle | Amira Sami Sara El-Metwally M. Z. Rashad MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS reads BMC Bioinformatics Next-generation sequencing Error filtration Machine learning Classification Feature extraction |
| title | MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS reads |
| title_full | MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS reads |
| title_fullStr | MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS reads |
| title_full_unstemmed | MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS reads |
| title_short | MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS reads |
| title_sort | mac errorreads machine learning assisted classifier for filtering erroneous ngs reads |
| topic | Next-generation sequencing Error filtration Machine learning Classification Feature extraction |
| url | https://doi.org/10.1186/s12859-024-05681-1 |
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