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pathMap: a path-based mapping tool for long noisy reads with high sensitivity.
- Source :
-
Briefings in Bioinformatics . Mar2024, Vol. 25 Issue 2, p1-10. 10p. - Publication Year :
- 2024
-
Abstract
- With the rapid development of single-molecule sequencing (SMS) technologies, the output read length is continuously increasing. Mapping such reads onto a reference genome is one of the most fundamental tasks in sequence analysis. Mapping sensitivity is becoming a major concern since high sensitivity can detect more aligned regions on the reference and obtain more aligned bases, which are useful for downstream analysis. In this study, we present pathMap, a novel k -mer graph-based mapper that is specifically designed for mapping SMS reads with high sensitivity. By viewing the alignment chain as a path containing as many anchors as possible in the matched k -mer graph, pathMap treats chaining as a path selection problem in the directed graph. pathMap iteratively searches the longest path in the remaining nodes; more candidate chains with high quality can be effectively detected and aligned. Compared to other state-of-the-art mapping methods such as minimap2 and Winnowmap2, experiment results on simulated and real-life datasets demonstrate that pathMap obtains the number of mapped chains at least 11.50% more than its closest competitor and increases the mapping sensitivity by 17.28% and 13.84% of bases over the next-best mapper for Pacific Biosciences and Oxford Nanopore sequencing data, respectively. In addition, pathMap is more robust to sequence errors and more sensitive to species- and strain-specific identification of pathogens using MinION reads. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 14675463
- Volume :
- 25
- Issue :
- 2
- Database :
- Academic Search Index
- Journal :
- Briefings in Bioinformatics
- Publication Type :
- Academic Journal
- Accession number :
- 176218895
- Full Text :
- https://doi.org/10.1093/bib/bbae107