Journal
BIOINFORMATICS
Volume 37, Issue 17, Pages 2744-2746Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btab076
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Funding
- National Science and Engineering Research Council (NSERC)
- Canada Foundation for Innovation
- Genome Canada/Genome Alberta
- Alberta Children's Hospital Research Institute Postdoctoral Fellowship
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WgLink is a tool that can reconstruct whole viral genomes with high accuracy, consuming significantly less memory and fewer CPU hours compared to existing methods.
Many tools can reconstruct viral sequences based on next-generation sequencing reads. Although existing tools effectively recover local regions, their accuracy suffers when reconstructing the whole viral genomes (strains). Moreover, they consume significant memory when the sequencing coverage is high or when the genome size is large. We present WgLink to meet this challenge. WgLink takes local reconstructions produced by other tools as input and patches the resulting segments together into coherent whole-genome strains. We accomplish this using an L-0+L-1-regularized regression, synthesizing variant allele frequency data with physical linkage between multiple variants spanning multiple regions simultaneously. WgLink achieves higher accuracy than existing tools both on simulated and on real datasets while using significantly less memory (RAM) and fewer CPU hours.
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