Reassembling haplotypes in a mixture of pooled amplicons when the relative concentrations are known: A proof-of-concept study on the efficient design of next-generation sequencing strategies.

ABSTRACT: Next-generation sequencing can be costly and labour intensive. Usually, the sequencing cost per sample is reduced by pooling amplified DNA = amplicons) derived from different individuals on the same sequencing lane. Barcodes unique to each amplicon permit short-read sequences to be assigned appropriately. However, the cost of the library preparation increases with the number of barcodes used. We propose an alternative to barcoding: by using different known proportions of individually-derived amplicons in a pooled sample, each is characterised a priori by an expected depth of coverage. We have developed a Hidden Markov Model that uses these expected proportions to reconstruct the input sequences. We apply this method to pools of mitochondrial DNA amplicons extracted from kangaroo meat, genu

SUBMITTER: Ranjard L 

PROVIDER: S-EPMC5886459 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature