Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs.

ABSTRACT:

Background

Reference sequences play a vital role in next-generation sequencing (NGS), impacting mapping quality during genome analyses. However, reference genomes usually do not represent the full range of genetic diversity of a species as a result of geographical divergence and independent demographic events of different populations. For the mitochondrial genome (mitogenome), which occurs in high copy numbers in cells and is strictly maternally inherited, an optimal reference sequence has the potential to make mitogenome alignment both more accurate and more efficient. In this study, we used three different types of reference sequences for mitogenome mapping, i.e., the commonly used reference sequence (CU-ref), the breed-specific reference sequence (BS-ref) and the sample-specific

SUBMITTER: Wang D 

PROVIDER: S-EPMC8507312 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature