BBMerge – Accurate paired shotgun read merging via overlap
Merging paired-end shotgun reads generated on high-throughput sequencing platforms can substantially improve various subsequent bioinformatics processes, including genome assembly, binning, mapping, annotation, and clustering for taxonomic analysis. With the inexorable growth of sequence data volume and CPU core counts, the speed and scalability of read-processing tools becomes ever-more important. The accuracy of shotgun read merging is crucial as well, as errors introduced by incorrect merging percolate through to reduce the quality of downstream analysis. Thus, we designed a new tool to maximize accuracy and minimize processing time, allowing the use of read merging on larger datasets, and in analyses highly sensitive to errors. We present BBMerge, a new merging tool for paired-end shotgun sequence data. We benchmark BBMerge by comparison with eight other widely used merging tools, assessing speed, accuracy and scalability. Evaluations of both synthetic and real-world datasets demonstrate that BBMerge produces merged shotgun reads with greater accuracy and at higher speed than any existing merging tool examined. BBMerge also provides the ability to merge non-overlapping shotgun read pairs by using k-mer frequency information to assemble the unsequenced gap between reads, achieving a significantly higher merge rate while maintaining or increasing accuracy.
- Research Organization:
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); National Renewable Energy Laboratory (NREL), Golden, CO (United States)
- Sponsoring Organization:
- USDOE Office of Science (SC)
- Grant/Contract Number:
- AC02-05CH11231; AC36-08GO28308
- OSTI ID:
- 1405052
- Alternate ID(s):
- OSTI ID: 1407458
- Report Number(s):
- NREL/JA-2C00-70437; 10.1371/journal.pone.0185056
- Journal Information:
- PLoS ONE, Journal Name: PLoS ONE Vol. 12 Journal Issue: 10; ISSN 1932-6203
- Publisher:
- Public Library of Science (PLoS)Copyright Statement
- Country of Publication:
- United States
- Language:
- English
Web of Science
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