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SRPRISM (Single Read Paired Read Indel Substitution Minimizer): an efficient aligner for assemblies with explicit
Aleksandr Morgulis1, Richa Agarwala1
1National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike Bethesda, MD 20894, USA.
Gigascience
|April 22, 2020
Summary
SRPRISM is a new read alignment tool that supports complex genome assemblies and offers explicit output guarantees. It outperforms other tools in sensitivity and accuracy for next-generation sequencing data analysis.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Next-generation sequencing (NGS) read alignment is crucial for data analysis.
- Existing tools often lack output guarantees and struggle with complex genome assemblies like GRCh38.
- Need for alignment tools supporting alternate sequences and explicit result criteria.
Purpose of the Study:
- Introduce SRPRISM (Single Read Paired Read Indel Substitution Minimizer), a novel read alignment tool.
- Address limitations of current alignment tools regarding output guarantees and genome assembly support.
- Evaluate SRPRISM's performance against established alignment tools.
Main Methods:
- Developed SRPRISM with features for handling alternate genome sequences and partial read alignment.
- Compared SRPRISM against GEM, Kart, STAR, BWA-MEM, Bowtie2, Hobbes, and Yara.
- Utilized benchmark datasets for single and paired reads (100 and 250 bp) generated with DWGSIM.
Main Results:
- SRPRISM achieved superior alignment results for error rates up to ~2.5%.
- GEM demonstrated better performance for higher error rates.
- SRPRISM exhibited higher sensitivity compared to other tools, even when optimized for speed.
Conclusions:
- SRPRISM is a flexible read mapping tool providing explicit guarantees on alignment results.
- SRPRISM offers advanced features for analyzing complex genomic data.
- SRPRISM represents a significant advancement in NGS data analysis tools.
