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The effect of variant interference on de novo assembly for viral deep sequencing
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June 22 2020
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Source: BMC Genomics. 21
[PDF-1.69 MB]
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Alternative Title:BMC Genomics
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Personal Author:
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Description:Background
Viruses have high mutation rates and generally exist as a mixture of variants in biological samples. Next-generation sequencing (NGS) approaches have surpassed Sanger for generating long viral sequences, yet how variants affect NGS de novo assembly remains largely unexplored.
Results
Our results from > 15,000 simulated experiments showed that presence of variants can turn an assembly of one genome into tens to thousands of contigs. This “variant interference” (VI) is highly consistent and reproducible by ten commonly-used de novo assemblers, and occurs over a range of genome length, read length, and GC content. The main driver of VI is pairwise identities between viral variants. These findings were further supported by in silico simulations, where selective removal of minor variant reads from clinical datasets allow the “rescue” of full viral genomes from fragmented contigs.
Conclusions
These results call for careful interpretation of contigs and contig numbers from de novo assembly in viral deep sequencing.
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Pubmed ID:32571214
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Pubmed Central ID:PMC7306937
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Document Type:
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Volume:21
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