Source-linked AI summary
SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner
Ruibang Luo, Thomas Wong, Jianqiao Zhu, Chi-Man Liu, Edward Wu, Lap-Kei Lee, Haoxiang Lin, Wenjuan Zhu, David W. Cheung, Hing-Fung Ting, Siu-Ming Yiu, Chang Yu, Yingrui Li, Ruiqiang Li, Tak-Wah Lam
TL;DR
Short-read alignment is evaluated for sensitivity using correctly aligned reads. The paper describes a paired-end alignment approach that combines 2way-BWT with dynamic programming, with sensitivity reported as correctly aligned reads.
Problem
The supplied passages frame short-read alignment as requiring sensitivity evaluation using correctly aligned reads.
Method
SOAP3-dp combines 2way-BWT seed alignment with dynamic programming to align paired-end reads, including reads with unmapped ends.
Results
Sensitivity is evaluated by measuring correctly aligned reads.
Takeaways & Limitations
The evaluation focuses on how many paired-end reads are correctly aligned.
Abstract
from arXiv · showhide
To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, GEM and GPU-based aligners including BarraCUDA and CUSHAW, SOAP3-dp is two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads with different lengths. Transcending its predecessor SOAP3, which does not allow gapped alignment, SOAP3-dp by default tolerates alignment similarity as low as 60 percent. Real data evaluation using human genome demonstrates SOAP3-dp's power to enable more authentic variants and longer Indels to be discovered. Fosmid sequencing shows a 9.1 percent FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides a scoring scheme same as BWA, which enables it to be integrated into existing analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and Tianhe-1A.
Step 1: Use 2way-BWT to align pair-ended reads
The alignment procedure uses 2way-BWT and dynamic programming in successive steps to handle paired-end reads according to whether zero, one, or both ends are initially mapped. For doubly unmapped reads, it locates seed alignments, pairs them, and applies DP to align both ends.
- Step 2: Align one unmapped end: Step 2 applies DP to align an unmapped end when its mate is already mapped.
- Step 2: Align one unmapped end: Step 2 identifies a candidate region for the unmapped end before alignment.
- Step 3: Align both unmapped ends: Step 3 uses 2way-BWT to locate seeds and then DP to align both ends when neither end is mapped.
- Step 3: Align both unmapped ends: The method pairs the seed alignments before determining the paired-end alignment.
CUSHAW2& · SOAP3DP BWA
The supplied passages list aligners and evaluation labels associated with CUSHAW2& and SOAP3DP BWA, including incorrect alignments and indel-length distributions.
- CUSHAW2&: GEM& is labeled “Fast&Mapping:&adap;ve.”
- SOAP3DP BWA: The supplied material does not provide additional textual findings for the SOAP3DP BWA subsection.
- CUSHAW2&: The evaluation includes the metric “# of incorrectly aligned reads.”
- CUSHAW2&: The listed aligners are BWA, Bow.e2, SOAP3-‐dp, GEM, SeqAlto, Barracuda, and CUSHAW2.
- CUSHAW2&: The analysis includes an “Indel length distribuAon (>20bp).”